I have finally found a replacement transmission. I decided to stick with an Automatic and ordered it up today. I was looking at a manual, but when I showed up to the salvage yard the prices for the transmission, shifter, linkages, etc were just too much at this point. It's fall now and the good working days are numbered and I know I can replace the Automatic transmission in 6 or so hours, so that's the way I went.
The transmission is from a 1998 Civic and has 104,000 miles on it. It was still in the donor car so I couldn't bring it home today, but it's supposed to be out and ready for me tomorrow. I will be doing all the proper transmission care, checking all the sensors and draining all the ATF and replacing it with all the new ATF I bought, but only used a small amount of it.