I found this build on Fishy Wargaming's site and I would like to play it tomorrow at a store tournament.

Decimator RAC-46, Dauntless-2, VI-1, Kylo-3, Saboteur-2, Moff Jerjerrod-2, EU-4 (60)

Upsilon Lt. Dormitz-31, Collision Detector-0, Hyper Comm Scanner-1, Emperor-8 (40)

However, is Engine Upgrade really better suited on the Decimator or can it be more useful on the Upsilon to help bring the 4-dice attack to bear when trying to turn around?

Also, I understand the Emperor is there to help push Kylo's ability through and ensure Saboteur works, but is Gunner with FCS another viable option instead if I get rid of Collision Detector and Palpatine?

Gunner and FCS can work just fine instead of Palptine, if you want the Upsilon to be dealing the crits. But generally with Kylo and a VI RAC, you want RAC to be slapping that Blinded Pilot down at PS 10.