1- Look under "ufos:" in XCom1Ruleset.rul, you will find all the UFOs defined there. The IDs are pretty obvious (ex.: small scout = STR_SMALL_SCOUT)
2- I suggest you look into Haral_Gray's Mechtoid mod, or Robin's MIB mod, both of which define new races, new race exclusive weapons and race exclusive missions. I think the way it works is that when you define a mission, you define what weapons aliens on that mission will have, so you would need to define, say, Altoid-Research, which only Altoids conduct and on which Altoid weapons are used. This won't change anything for any other mission, so the regular aliens won't change.
3- The mission weight represents the relative chance that a given mission is picked for a given month in a given region. Looking at the ruleset, I would guess that the game first picks a region using "regionWeight", then picks a mission using that region's "missionWeights", then picks a race according to the "raceWeights" of that mission.
That means you can't prevent one of your Altoid missions from being picked in January, the fix to that is to give raceWeights to sectoids and/or floaters only for the early months, then switch to Altoids later. In the mission's raceWeights, the first number (ex.: "0:") is the number of months since January (0 = January itself), then the weights represent the relative chance of that race being picked. I don't think it is percentages, but rather if I say "STR_SECTOID: 3" then "STR_FLOATER: 1", then I have 3 times more chance to see sectoids. If I use 4 & 3, then I have a bit higher than 50% to see sectoids, etc.
4- You can make clips manufacturable without the weapon, you just have to not define a manufacture project defined for the weapon.
