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Find a schematic of the engine/transmission harnesses. There are some circuits that share grounds, or work in conjunction with others. It is possible this is causing an issue somewhere. If the fuse is blowing, there is a short somewhere; do some digging and see if you can locate it.

What happens all when it dies? Does it restart right away or not?
 

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Ethan, On a '93 with manual injection pump there is very little to no engine control function from the ECM. In fact, it is actually only a TCM in this application.

There is still a TPS (throttle position sensor) used for transmission control, and it could be possible that since there is no feedback from the transmission, as most of it is not connected, it can be creating some sort of electrical havoc here. What may need to be grounded that isn't anymore?
Schematics I have looked at do not fully illustrate what, if any, malfunction in the TCM can have on engine operation. Most of this is fully mechanical, with the exception of the fuel shutoff solenoid and lift pump and neither of these should be affected by the TCM.
If nothing else, I'd still say you should try to verify that nothing is compromising fuel delivery; severe blockage, faulty shutoff solenoid in the IP, bad OPS, and no massive air leak or failing lift pump.

In the long run, you'd probably have been better off installing a manual.
 
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