mixing mods:
when you merge mods you have to be very careful. you can mess up things and it will couse minidump or you just get unfair ship's hull or price or damage... you have to decide which specific files you coping over the default. make sure all the new ships, researches (what you defined in the player's entities) are in your mod's folder; all sounds, effect etc. (what you defined in ships', modules' entities) are also in your mod's folder. you need to check the language file for sins (string/english.str), has to be there all the entities' names and descriptions. and after this 99% sure that the new ships' icons etc are all messed up, couse in the mods usually the new ships and modules just using the old positions, only the textures are altered.
I don't want to scare you, but merging mods isn't easy. I advise you to make your own mod with your ideas, step by step with small changes. and after you know what is linking to what, how the playerentities, the planets, the ships etc. are working on the code level, you can mix up mods, and you will not lose your mind.
starbase, logistic & tactical slots:
you can mod these things through the planet's entities (PlanetTerran, PlanetIce...). At the end of the file there is a line "maxStarBaseCountPerPlayer 1"... just modify it as you wish.
as you see in these files are the planetupgrades. there are stages with descriptions for CivilianModules (logistic) and TacticalModules (tactical). you just have to change the maxModuleSlotCount value
good luck
neterw