HI my names Nate and i may now a little about the s12. (hence my name)
First s12's came in 2 generations MK1 and MK2. MK1's have either a CA18ET or a CA20E. (CA18ET was not offered in auto.) Mk2's Came with a CA20E and a VG30E in the SE model. Only in japan was there any other options, the FJ20ET. Even though the Engine code doesn't mention this the FJ20ET is a dual over head cam and is the older brother to the SR20DET.
Unfortunately a flush most likely will not help your transmission, but s12 parts are really cheap! To find a junk yard with a CA20E manual (c-trans) usually it is pretty easy and most likely you could purchase all the necessary parts for a manual swap for under 150bucks.(make sure you take the flywheel)
Also there is ALLOT of info on one of my favorite sites.
http://www.club-s12.org
All in all S12 are great and they have a awesome retro 80's tuner look. Buy it and have fun!