Excellent changes all in all, hitting the things meant to be hit and not anything else.
Bomb cooldown is still too low and the perilous overclock crit is not the biggest problem (if one at all?) with engi at this time i believe. Its the fact that he still easily has 2-3 bombs at all times + trollhamer and he can spam them with no FF damage and just demolish elite waves, patrols, chaos ones included and monsters ontop with very low risk and no potions.
What you ought to really do about the chaos wastes grudge marks, and banners, is to ensure they do not spawn in the first two maps, something like a shieldbreaker or a crippling stormfiend is too close to instant GG.
What most of these rarely used weapons need more than a bit of stamina, is actual cleave, average functionality. People will typically prefer a weapon that works against everything if that´s an option over something that is about equally good or even slightly better against most but worse against something notable.