I think your problems are pretty much with the ISC to start with. This device is on the left hand side of the carb and sets the curb idle (calculated by computor). Try to test is first, If you have troubble finding a new part try to match it up with a central fuel injection off af a 3.8 l unit. Code 63, the TPS could be out of range because the ISC isn't allowing the throttle to position itself correctly.
Code 41, 99% of the time is a vacuum leak or the feedback solinoid on the back of the carb is bad mechanicaly not electricaly. Ford dosen't support this part (feedback solinoid) however NAPA does, definitly a high wear item, and when the solinoid is not working it will make the engine seem like it needs a tune up.
EVP "EGR Valve Position" (EGR position sensor) code 31. There could be some junk underneath the seat on the EGR valve holding the EGR valve just a little bit open. This could also be the problem with the code 41 if the EGR valve isn't seating properly and leaking causing a lean condition. Start by cleaning the EGR valve.
First thing to do is test is the ISC. After the KOEO test is complete don't exit the test yet. The computor will enter the output state mode or test. this means every time you depress the throttle all outputs will change state including the ISC motor (this part will extend or retract and it is common for the part to break in one direction meaning that it will retract and not extend or get jamed), in addition the vacuum solinoids will change state underneath the plastic cover on the right hand fenderwell.
Lastly, Code 35 is linked to code 12, most likely.
Good luck and ask more questions or post your findings!