In order:
1. Yes, you can remove parts through a data.INI edit. An example:
This will 'hide' the part listed under ModelNodeName. However, the part listed under ParentComponentName must not exist on the LOD. However, you will not be able to use this part for anything else and if it's a moving part, you will not be able to substitute a moving part in it's place. In other words, if you hide the F-16A stabs, you can put an F-16C stab there, but you won't be able to move it at all.
2. To 'attach' a weapon to a moving part, do this:
Note the parts in bold...they determine which part of the model to 'attach' to, and how that part moves. Also, the SpecificStationCode can be used so that no other aircraft can use that particular 'weapon' and that weapon station can only load that particular 'weapon'. You will obviously need a properly matched weapon.
3. Yes, you need to guess, however, this tool can help you:
http://forum.combatace.com/files/file/6314-ruler-tool-for-the-thirdwire-sims/
It was specifically created to allow you to find coordinates on LODs where you don't have access to the original MAX file. It's mounted using the 'FakePilot' method. Use it, take screenshots and that will get you close.
Or, you can wait...various projects are in work.
FC