I don't know most of those mods, but if they include BH opponents there will be no balance. The vanilla ships and anything that comes from the more tame mods will be free money if you build with the more broken mods and the ships that come with the more broken mods will be unbeatable if you don't. Build mostly from whichever mod the ships that give you the most trouble with came with. I'm going to guess based on reputation that that's going to be ABH, 40k, or one of the Star Wars mods.
If you can get through vanilla BH I'd look out for Auto++ messing up your crew management by failing to interact with ammo or special batteries from mods. If your haulers are crossing half the ship to move ammo that you thought was being autoloaded your ship will underperform badly.
If one of those mods doesn't have unbeatable shields you have to rely on being fast enough to not be hit by the big stuff. If there's a weapon too fast to dodge and too long range to effectively kite that is stronger than the strongest shield you may have set yourself an unbeatable challenge.
