Federation ships with low damage? They're built of advanced metals that would seem almost like magic to the crude B5 humans. Phasers are sustained beams, mini-beam is stupid. They tend to be used to precise hits because the Federation characters are pussies, in a real way they go all-out though. Watch some of the DS9 episodes where they have proper battles.
Torpdoes wouldn't have e-mine, they'd be more like precise, SAP, TD, and QD for quantum torpedoes.
Phasers would be beam, DD, precise, pulsing phasers SAP, precise, TD. They're nastier, that's why they invented them.
Klingon and Romulan phase disruptors would be SAP, TD, with beam distruptors getting beam, TD. Torps the same as Federation, but Klingon Polaron torpedoes would bypass the shields trait.
Cloaking devices wouldbn't be stealth, you can't see through them at all, certainly not with B5 tech. They'd be more like hyperspace mastery, decloak where they like and open fire. Maybe rule it so you can't cloak again for X number of turns.