Electrical 93 computer system deletion.

I love when guys right away go to PNP mega squirt.

The issues from the old decrepit harness will follow into a new ecu .

Holley terminator efi for 5.0 seems right up your alley . Will use the same distributor and coil you already have . The harness may be a bit long for a ac cobra because it’s fox based but the system will do everything you want it to and then some .
 
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My experience, it's best to fix any issues you have (or at least properly diagnose the issue), before making changes to the system.

Would suck to put in a new megasquirt, just to find out you are having the same issue because of a bad O2 sensor or ECT sensor...
Then you have to deal with any issues with setting up the new system, while still fighting the unresolved issues with the old system.

Have you pulled codes?
 
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I recently pulled up a post by @jrichker that listed what values the air temp sensor and coolant temp sensor should read at certain degrees. As they replace the function of a carbureted car’s choke coil, it would make sense to check them, the connections and the wires. The computer could be getting bad info from them and not throw a code if they are off, but not quite dead yet. How cold is cold? The chart only goes to 50 degrees.