swapping an AT to a MT isn't that cost prohibitive, provided you do the swap yourself. I had the same problem in my 90 NA and eventually the car became undrivable and forced me to replace it. i bought everything new except for the tranny(obviously) and the pedals(brake/clutch), and my swap only cost me about $1000...and that included shipping(since i'm overseas shipping is real expensive). so i'd say check ebay for a tranny or start calling local junkyards and see if they have one. if you want more info on what's required for the swap, either contact me or check out this site. they sell a whole kit of everything you need for $1850(TT transmission). hope this helps
www.z1motorsports.com