I'm not sure of its the same problem i had when i replaced my first engine. I got the engine from a 98 contour, it bolted in but wouldn't start. It was an electrical issue don't exactly what it was, the mechanic tried for 2 days to get it to work with no luck. Ended up returning the engine and rebuilding the old one. I remember the mechanic telling me that he could've got the electrical issue solved but it would've been lots of work and that it was easier and cheaper to rebuilt my old engine and put it back in. I'll try to get hold of him this week and get some answers.

95 SE MTX Midnight Red
Dual Extrude Honed SVT Intake Manifold / 65mm TB / SC Cold Air Induction / Ford Racing 9mm Plug Wires / Quaife Limited Slip Differential / Centerforce Dual Friction Clutch / Fidanza Flywheel / UR Underdrive Pulley / Custom Dual Straight Flow Exhaust / StreetGlow Sport Pedals / Tint / Pioneer Deck and CD Changer / 2 12" Orion XTR subs / 2 MTX amps(425&280watts) / Phoenix Gold Titanium Bass Cube and Wiring / Boston Acoustic 5x7's, and Rockford Fosgate Tweeters. Next: 19# injectors and chip
Rebuilt engine @180,000 km
Rebuilt tranny @215,000 km