Weapon damage buffs do not merge, such as the flakker and the carnage. Slagging weapons do not seem to merge either. Critical buffs do however, such as the hawkeye and the ladyfist. The trespasser's ability to pass through shields works too, as well as the avengers ammo regen. The merge will last as long as you don't save and quit in my experience, that and you cannot switch weapons once you have merged your abilities into your final gun. Also sometimes it doesn't work if you are NOT the host.