Get a manual...which fuse is it blowing? I didnt look up your motor so just generalizing.
if it were at my shop I would do this:
1. Hook up a set of known good remote control and harness. Does it still blow fuse? If so we know it's on the motor side of harness.
2. Isolate and test each circuit of the suspect harness.
3. Test each system controlled by harness. (High pressure pump, lift pump if electric, TnT, lighting circuit, etc.)
4. Hook up diag software and see if emm communicates with software.
this is all played out in the manual. Granted, as a shop I have more available such as an extra set of controls and harnesses, the software and cables, manuals and the knowledge to use them. But, you can improvise and do alot of the preliminary by yourself.
I take care of many etecs. I have yet to replace an emm due to a motor blowing a fuse as the only issue. Never even heard of it and I know several wrenches that work with etecs. Yes, the emm may be bad but the fuse is probably a secondary issue. Ymmv.
edit to add, I think there is only the one fuse. I also think those had a pulse lift pump so no fuse there. The TnT switches may be fused but I just cant remember. I only see one of those 1st year 3 cylinders any more.