Just a quick essentials list for the final boss (imo)
Max Shields
Crew Teleporter with Two Mantis
Level 2 Cloaking
General Crew to Repair Things
Either missiles or lasers that shoot at least five shots combined (preferably much more)
Preferably lvl 2 sensors
Teleport your mantis to each weapon room at the final boss, start on the missile room and then ion and then lasers and then beams.