[capnq]

How can you give a single weapon a combat to-hit bonus without affecting all the weapons on the ship?

I think you'd have to design a separate Version of the weapon with the bonus, and add it to Components.txt while leaving the originals in there, too.

How can one edit the AIs to comply with a new mod?[...] What is a good way to test a mod?

Depends on the mod. Mods that don't change any techs or Advanced Traits shouldn't require any changes to the AI. Tech changes may mean rewriting the AIs to use the techs or counter them.

Playing lots of test games is the best way to go, either solo or with volunteer betatesters helping. You can also set up hotseat solo games with more than one empire under your control, if the AIs can't handle the mod.

How much do troops affect a populace's happiness, can this be modified, if so then how/where, and how can you tell that it does (other than watching the 400+ troops you just dropped on the rioting planet make it jubliant the next month)?

This is defined by the race's Happiness type; the numbers are in Data\Happiness.txt . Watching what the troops do is the only way to judge, unfortunately; there's no way to see what the actual Anger number for a planet is.