depends what engine the cl has, your existing box may fit. MK3 gtis never had 6 speed box, all 5 speed 
AFAIK, and I'll have to confirm this if I do into overhauling the engine further, mine is either engine code AAM or ANN. Bogstandard 1.8 engine, 5 speed, bought as a "doing up" project for a decent price.
Would the gearbox from this work alongside a 2.0 16V GTI engine if I did want to do an overhaul?
Obviously, I'll first start looking at replacing suspension, brakes, exhaust, air filter, wheels etc with decent parts and finish the cosmetic side of the car (it's just begun a paint job) before I invest any serious money into the engine, but any info you guys have on converting a standard CL to a GTI engine is very helpful and much appreicated :-)