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So, I've been looking over the wiring diagram in my FSM tonight and I have some bad news for you. The "engine" fuse is what supplies power to..., cruise, charging system, ignition system, MFI system, starting system, and theft system. So its hard to really narrow that down unfortunately. One way to help is to see which side is grounded out, causing the popped fuse. So if its popping fuses as soon as you stick them in connect the positive side of your DVOM to the battery + and the negative where the fuse terminals would go. If you get a 12v on one side and not the other, then thats the side that your issue is in.
I'm willing to bet you have a short to ground somewhere in your MFI circuit. The spots that I'm looking at on my FSM are going to be from the fuse box to the junction block((A-83) which is wrapped in plastic underneath the fuse box), the transaxle range switch(if your auto), from the junction block to the ASD relays, from the ASD relays to the fuel pump, and another to another one of the ASD relays, to another junction block(A-82, under the fuse box) then to your ECU, your alternator, your ignition coil, your O2 sensor, and your injectors.
So if you have messed with any areas of the harness that is listed about that would be the first place to check your wiring. If you still haven't figured it out by Sunday/Monday let me know(I think your in Columbia) and I can ride down and help you figured it out(I may need some gas money ) If you need me to elaborate on anything that I've said above just let me know and I'll try to explain it in better detail! Good luck!
EDIT: My FSM is a 1998 Talon FSM, so while everything should be the same, just wanted to throw that disclaimer out there.
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