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It could be your fuel pump.
Did you replace the thermostat with a generic part? That's what I did with no results. Try replacing with original Ford parts. That did the trick for my 93 Escort.
I had a similar problem with my 93 Escort although the fan would run intermitently. I had the fan switch changed several times with no luck. One mechanic finally nailed it to generic parts. I guess there is a bulletin out to replace the fan switch with Ford parts ONLY (the generic has play in the mechanism). Now the fan kicks in like it used to and the engine runs great again!
I had this problem with my 93 Escort. The exhaust manifold may have a vacuum leak. I'm guessing this may have caused the O2 sensor to overload. Check for vacuum leaks and replace the O2 sensor if necessary.
Check the battery cables. They could be coroded where you may not see it. Also check other wires for shorts or corosion.