I changed my tranny fluid like a month ago and that helped the rough shifting a little. I didn't think of the short throw shifter. Could it be that the short throw shifter isn't hooked up right or a crappy ebay one (my guess a cheap ebay one)? The kid that owned this car before me didn't care about this car/maintain it...Hes the one that put in teh short throw. I've been noticing more stuff wrong with my car from the kid ...(wing off centerd/leaking, mud guards missing, and hell the whole wiring harness was melted when I bought it 8 months ago).

 

Elaborate a little more on the rough shifting? Does that mean it grinds when engaging, or just a lot of resistance, or does it make a noise (not like grinding) when shifting? It *could* be the shifter, if the bushings are way loose, so check to see if you have slop in the shifter. Check play at the shifter mechanism on the transmission too. Otherwise, check the clutch pedal freeplay. Adjust the freeplay at the pushrod. Should be around 1/2" IIRC. Also make sure you have good quality fluid in your transmission as well. Cheap gear oil can cause more problems than one might think.

I changed my clutch, machined the flywheel, lubricated the shifter mechanism on top of the trans, replaced the clutch release lever bushings, chopped my shifter, and replaced the gear oil with Royal Purple, and the car has never shifted better. I used to have alot of resistance going in first, and would scratch 2nd and 3rd alot. After doing all that, it's like driving a whole new car.