This is a bit awkward--it is inappropriate for me to help a player design a ritual, or tell him what bonuses he ought to get for what. It is not inappropriate for me to discuss such questions with a referee trying to understand the mechanics of the game. I'm going to approach this from the latter perspective, and attempt not to address anything that is directly significant to your game.
Is thought projection or telepathy considered as native tongue?
I would say that to my mind, they are the same as thinking but not speaking, and thus the spell would take a penalty for not having a verbal component. Against this there would be a bonus for the requirement of the successful use of a skill--you must successfully activate the telepathy/thought projection skill for the primary skill to have any chance of working, and you get one shot at it. I would also allow a bonus for appropriateness in the thoughts expressed, if they were appropriate and there was not any other bonus for appropriateness built into the ritual. Since no words are spoken, no other speech-based bonuses can apply.
Would it considered as loud if the distance of the thought projection is the same as speaking loudly?
Although this question may have been mooted by the previous answer, I feel it necessary to clarify a distinction. The default for telepathy and thought projection is "narrowcasting", that is, targeting select individual minds with a penalty for select multiple minds. There is a "broadcasting" variant which attempts to convey thoughts to all minds within range. If it is telepathy, it is not the equivalent of speaking, and it must be made clear that if you were to perform a broadcast telepathy skill (if the referee allowed such a configuration without prohibitive penalties) you would be opening two-way communication to every mind of the appropriate class (human, humanoid, animal, alien are the four classes, not counting self) within range. You would be very fortunate if you were able to complete the ritual with that much potential distraction. An open channel to all classes would have to be at the bias of that of the highest class. As for broadcast thought projection, it would face the penalties for the highest-penalty class present, and the referee might require that the alien minds present must be able to "hear" the thoughts for them to be considered "spoken". I would not normally allow thought projection to stand for speech, but might make an exception for a creature for whom thought projection was its normal mode of speech. (I know I said I wasn't going to comment on your game, but it has been my impression for quite a while that it is Gamma World on the other side of that rift, and that is an example of a world in which thought projection is the normal mode of speech for a large number of indigs. That does not make it the natural mode of speech for you.)
I do not think that I would differentiate "loud" on the basis of range. The point of "loud" is primarily that the enemy can hear it and understand it--you can't whisper the words under your breath and hope he doesn't know you're casting a spell, but must cast the spell dramatically and obviously. Thought projection never sounds "loud" in the minds of those who receive it, and thus it lacks the drama required.
What would be the penalty and bonus for a unison prayer?
Technically, a "unison prayer" as such is a separate skill that permits the combining of magical powers of several skilled users. The potency of such a skill lies largely in the facts that the highest scores of any member within the group are used for each skill regardless of which user is initiating it, and that each member of the group can perform a skill simultaneously based on the support of that union. It is a very high biased skill, intended to be impossible in most worlds where magic is not itself extremely high.
There are two work-arounds.
One is to say that everyone is performing this skill, and each person involved gets to roll for whether he successfully performs it. Assuming that everyone has a high enough chance of success, this increases the chance of success more than it increases the chance to botch; however, it means unskilled individuals create a significant level of risk, as their chance to botch is likely to be greater than their chance of success.
The other is to treat the "others" as "necessary material components". You then must specify how many "others" are required, the skill will not work without them, and you will be bonused according to the value the referee chooses to place on "one person willingly participating" as a material component. My personal inclination on this element is that it loses value as the volume increases. A ten carat diamond is not worth ten times as much as a one carat diamond. At some point the material component morphs from being "two people" to being "several people" to being "a small crowd" or "a large crowd", and the value of more people to "a large crowd" is not as great as the value of more people to "two people".
If at least one person is expected and one person participates would this penalize the skill?
I think this is covered above, but for clarity if the skill requires "at least one person" you get bonused for one person, and you do not get additional bonused for one million persons because they are not part of the bonus; if it specifies "one million persons" and you get nine hundred thousand nine hundred ninety-nine, the skill fails for want of the required material component. If it specifies "at least one (additional) person" then it stands or falls on whether you have that one additional person, and the only advantage of having two is that if you lose one you still have one.
What are the bonus for additional participants?
There are no bonuses for having material components that are not required by the spell. There is no provision made for optional components to increase a spell's chance of success.
The nearest you can get to this is to devise a variant of a "targeting skill", a separate skill which is performed by you before the main skill, in which you include some specified number of persons and if successful you get a bonus on the next skill or the next casting of a skill of a particular identified type. The general ones are more useful, but cannot be chained. That is, you could logically design a skill that will give you +10 to the next magic skill of any sort, but if you cast it twice in a row the success of the first casting is spent on the second casting. You could instead design a skill that will give you +10 on the next casting of specific spell X, and cast it multiple times to build up a "charge". There would be a duration imposed on such a skill, though, so you couldn't charge up all week in preparation for a single super-bonused casting. (At the least, I would require that all material components for each casting be unique until the charge from them is spent.)
If the participants are asked to say things in their own language, would this be considered as native language for the participants but is a language other than character native tongue relative to the caster?
A language is magical if the person speaking it considers it magical.
Would it count as spoken loudly if the participants are the one who does it?
It is spoken loudly if it has the dramatic effect of alerting others to the fact that you are casting a spell.
Would the participants body involvement counts as additional bonus?
That's a referee's call. If the referee wants to count "person willingly performing bodily movements in furtherance of the casting of the spell" as worth more than "person willingly involved in furthering the casting of the spell" he can add a point for that, provided no single material component is worth more than 10 points unless it is destroyed in the casting.
If the participants are asked to spin around while carrying the body of the caster, would this count as full body involvement?
Not for the caster, and for the others it's not relevant.
If the ritual is physically exhausting for the participants other than the caster, would this count as additional bonus?
Probably not, but that's a referee's call. After all, the point is that you are "using" people as a material component in a spell. If you sacrificed them their value would double because they were destroyed in the casting. If they are not destroyed in the casting, it is very doubtful that you can increase their value much over the simple fact that you are using them.
The caster would not be "physically" exhausted because the caster is in spirit form but would feel exhausted if the caster returns to the body. If that is the case, would that counts as additional bonus?
The point of exhaustion is that the caster is temporarily crippled and cannot perform any other actions without difficult attribute checks (and a serious motivating factor like life-or-death). It is entirely possible for the caster's spirit to be completely exhausted and unable to move or act under its own power. The notion that the person would be exhausted if (and only if) he returned to the body is not a detriment, because the caster can avoid the exhaustion simply by not returning to the body.
Does the rift sealing ritual penalized for including a second skill?
If it is then what is the second skill?
The rift sealing is bonused if it requires the successful use of a skill for which a roll is normally required. That is at times a judgment call. For example, if the roll calls for you shouting the name of your enemy and there is reason why at this moment you might not be able to shout, the referee could require a skill check (sonic signal generation, most likely) to determine whether you can cast the spell based on whether you can shout the name. (If the sound is not necessary, going through the motions of shouting the name and failing to do so might not prevent the casting of the spell, but failing to attempt to shout the name would.) Since, though, player characters generally have professional levels at talking, they don't have to roll to speak the required words of their spells, and the issue is assumed. Similarly, simple movements such as holding, lifting, or touching a small object, turning around, stepping in a simple pattern, or other movements are not rolled and are not at issue, unless there is a reason they might not succeed in the present circumstance.
Conversely, if the caster is an amateur dancer and he makes one of the action components of the skill a successful eight-turn pirouette, the referee will properly require that the character make a successful dancing skill check when he attempts to cast the spell, but will also appropriately include a +10 bonus on the chance of success on the skill itself for incorporating the pirouette. The logic here is that if the pirouette fails the spell cannot succeed, so the success of the spell has been made dependent on the success of the dance, a limiting factor. If the caster were an expert dancer who can do eight-turn pirouettes flawlessly and effortlessly, the referee would not include the bonus because he will not require the roll. If the caster having designed such a spell eventually becomes an expert dancer, he will still get the bonus, but he will still have to roll the skill when he is casting the spell to prove that at this moment he was able to perform the pirouette as required.
If the casting of this spell requires the success of some other spell, the referee will bonus this +10 but will require that the other skill roll be successful or this one will fail automatically and have to be restarted from the beginning.
I hope this helps, and I hope I haven't stepped on Scott's toes with this.
--M. J. Young