Swapping ECUs is not hard. They're located under the dash on the driver's side. Takes about 2 minutes to get it out, mostly due to wire loom stiffness. 10mm (or 8mm) bolt that holds the harness connector on. Unbolt, slide the connector apart, and wiggle the ECU out of its shelf.
As for what replacement, any year CFI should work, and I've used automatic ECUs in manual cars (the upshift light even works).
However, I doubt it's the ECU, and if it is, the culprit would probably be a leaky electrolytic capacitor (which can be cleaned/fixed very cheaply if you or a friend have the skills). My guess is the injector is stuck open a bit, perhaps adding too much fuel, the TPS may be faulty. Check the distributor for wobble or egg-shaped wear on the rotor button - that can cause intermittent spark strength/timing, which will cause backfire. Most importantly, check the mechanical timing. If the belt was loose or worn, and jumped 1 or two teeth, the engine would start running very oddly, with sporadic response, acting like it was missing a cylinder, very low power. The engine would still run, but pretty badly, and very often will also backfire right out the intake on a CFI. Each tooth represents 4 degrees of cam timing, so it can cause a pretty large effect, very quickly if the jump is sudden.
Just some late-night thoughts.....