John,
I've seen some ships with defective Zener diodes draw way too much current.
You need to plumb the ship into the 6.3V GI as the ship REQUIRES AC voltage to function. IE the cannon and/or engines won't blink as you saw.
I'd recommend at a minimum you check out my installation instructions for my WingLEDs:
http://Pinball-Mods.com/url/stngWingLED