Background on the Car:
A 1995 Eclipse GS Automatic with over 195,000 miles on it.
When I bought the car I was told an engine and “maybe a transmission?” swap from a 1996-1997 GS/RS. I'm unsure what was swapped besides the block and fuel rail. From what I can tell, the people that did this swap had little to no knowledge of differences between years; I realized this when I found the car had no fuel pressure regulator due to the change in location from 1995 to 1996.

Old Transmission Issues:
The transmission worked fine for the first 6 months of owning the car, then rough shifting started to occur that would send the car into limp mode. I took it to a transmission shop where they told me I needed a new transmission. I went ahead and let them put a rebuilt transmission in. When the swap was done they told me the inside of my old transmission was filled with crevices. “Yeah…sure…”

New Transmission and Issues:
After a few days with the new transmission, the car once again started having the same describer above. Still being under the 6-month warranty, I took it back to that shop where they fiddled with it for a few days and said they fixed it. A few days later the issues started again, but this time the shop blamed it on the IAC/IAT sensor codes the car was throwing. “Which is still there today.” After a little research, I found there was little to no connection between the sensors and the transmission. With a little persuasion, I got the shop to look at the car again. This time around the problem was fixed until the warranty went out.

Final Problems After Warranty Expired:
After researching problems on this forum, I came to the conclusion that the problem was the input speed sensor. Once replaced, the speed sensor did lessen the limp mode problem and completely fixed the rough shifting. The limp mode now only happens during heavy acceleration in second gear, where it just simply will not shift up or down after done with no indication.

I am at a loss. This is my first car and I do not want to part with it, but if I cannot fix this problem I will have to sell the car and buy an Eco friendly car to finish up college. I seriously do not want to do that!

I need your help pinpointing the issue… Any suggestions?