My
configuration is also very similar to what you guys are running. Agreed that the two huge multi's are the way to go (at least for me).
What problem are you having with Chaff? Yes it's an annoying delay to the kill, but not much more. When an NPC chaff's, I use that time to fill my capacitors. You can also still attack him by deselecting the target and firing your weapons in 'fixed' mode. I don't typically do that, but wanted to mention the option.
BTW, my Vette is vanilla.... no engineer upgrades.