1) Has anyone figured out how to change the names of different stats?

They're all in english.str.

2) How does one go about tweaking the research tree? Is it possible to lift or tinker with the one facility per research tier idea? IE perhaps it could be a number of planets colonized to unlock a new research tier, or a research technology (like advancing an age in AOE).

You can change all the research on the tree, you can make things happen every other research tier, whatever. You can't make the other sort of changes to it afaik.

3) Phase lanes seem pretty hardwired into the game as a way to get around. Has anyone figured out anyway to 'disconnect' planets? I think maybe tweaking with the phase stabilizer rules might be able to do it, but I haven't for the life of me figured out how those work either.

Yeah, you could probably make a system wherein building a basic structure like a metal extractor or something always makes a phase lane there with the Vasari ability, or one invisible structure that does the same placed in all your mod's maps.

4) What about the visibility system, like which planets one can "see." For example, everybody can see the star in their system, and you only see the planets connected to some wormholes after jumping through them... Where do these rules live? Additionally, their are three stages of visibility, the greay "you know I'm here but what am I", the "recently observed" and the "you can see me!" I know that a status effect can give LOS, is this only a planet status effect, or is it possible to move this effect to ships?

Don't know, will be investigating that.

5)Where do the 'jump type category' (Wormhole, star, or planet" rules for the planetary bodys live?

Not sure what you mean here? I think the advanced jump abilities just set a entityModifier that you can jump to stars and wormholes.

6) I've noted the 'CanFireAtFighter:" tag for weapons. Is there such a tag for cap ships/frigates?

Yes, this works on all weapons.

7) Is there a way to set "If ability A is active, ability B must be inactive" clauses? Specifically I want to develop ammunition types for units with different effects, so you could switch between say "target their engines!" Or maybe incindiary ammo, or something. But obviously that sort of unit would get overpowered really quickly if they could use all the ammo types at once, soo...

You can could set some sort of over time disableAbilities or make it deplete all the antimatter. There's probably another way to do it with end conditions though.

8) What dictates AI target acquisition? I assume damage type, but I am unsure.

Dunno, I'd assume that too.

Pretty sure the "jump to all stars" thing is hard-coded.