Whether its a hard fix or not would 'depend'. If the problem is -inside- the tranny, then the fix involves removing the whole tranny. Thats probably 30% of the job of changing to a 5 speed. (The other 70 %, in my view, would be making the other changes to the car to let it work with the 5 speed, and installing the 5 speed intp the car). I only know about the 1.9L Escort LX's. The Service Manual for them says you take the 5 speed tranny out together with the motor - though others on the forums have apparently taken 5 speeds out by letting it drop down below the edge of the driver's side 'frame' on the side of the engine compartment. The auto tranny can go in and out with the engine in place, just held up at the flywheel end.
Im pretty sure there is a 'how-to' & more than a couple of threads about chaing to the manual transmission. Right now all I can say is that you may be able to drive the car indefinitely, if the problem is just the SES light, or a TCC that stopped locking-up.
I know the ignition switch mechanisms (in the 1.9L Escorts) are slightly different, but the differences have to do with safety/security 'interlocks'. For instance, you have to put the shift lever in park to remove the ignition key on an automatic, but with the manual tranny, the ignition switch has to be pushed in a millimeter, in order to turn the key all the way to where it will come out.
The computer is also different. The computer for the auto tranny would be expecting input from the transmission, and might turn the SES light if it doesnt see the input from the 'turbine speed sensor' in the tranny. So there are some differences in the wiring harnesses too.
I use two Escorts, both 2nd gens, both 1.9L wagons. The one we use in the suburbs of the nation's capitol has the automatic tranny - since we spend a lot of time in darned heavy traffic, and I dont want to be shifting so much. The other one we keep in S. Texas, where there isnt much traffic, so shifting is a pleasure, not a burden.
If wanted a 5 speed instead of an automatic, I would start with one from a dry & salt free state (Arizone for instance, not upstate New York) that was already a 5 speed..... with a worn out clutch to keep the price low.