Is the engine something like a 2.0L conversion, you know, ABA bottom with 1.8L head and some things swapped and some not (like in the ignition distributor and intermediate shaft areas)? I ask because I don't know what engine you have for one. Because you swapped the trans and clutch so I guess you can assume no mistakes there as it did it before the swap. And because with the 2.0L if you mis-match some of the parts the crankshaft can slide just a little and cause some knocking interference. Has to do with the intermediate shafts, if it is the 1.8L one, not having the gear cut down and/or bad trust bearings in the engine.