Engine Upgrade, was a bit wasted against a higher PS ship, I didn't feel like I got much use out of it, and it didn't mesh well with Stay on Target, I would have preferred something else in this particular game (probably Stealth Device or ACD).
Using Stay On Target leaves you stressed - so Advanced Cloaking Device wouldn't be useful on the same turn you used Stay On Target. Stealth Device..... if you're being shot at cloaked you should be fine, if uncloaked I'm unconvinced one extra agility will do much to save you.
Stygium might work nicely because sooner or later you may well have to accept mutual shots to get any - plus it still gives you some protection if you have to stay on target and your opponent still gets a shot somehow.