Sounds like a misalignment but you said that the clutch pedal is smooth and disengages fine? If the clutch is missaligned its almost impossible to mate the eng/trans as the input shaft wouldn't be able to slide into the pilot bearing. How about the clutch fork pin? Is it in all the way? I know ppl that didn't get it in all the way and it came out and broke the sleeve for the pin. If your shift linkage is wrong it would definetly feel wrong and you would know. How was the condition of your old pressure plate?