2. can i add more banks to cap ships so they can be more like starbases , shooting at more than 1-2 targets?i read it could upset the game horribly
You can just make sure you only increase the banks that are currently set. Look at my flagship mod for an example.
3. i would like to make so ever planet has a bonus or relic of some type if possible which file(s) do i mod and how?
I believe you should look at the *.galaxy file for each map you want to use...
planetArtifactDensity
&
planetBonusDensity
Edit- Well Harpo beat me to the punch while I had this open 