No shifting possible

[karospirit]

I have a 2003 1500 Nomad that leaked oil. The guy I brought it to to fix the oil leak has had to lift the engine and drop it to get to the oil leaks. Oil leaks are fixed. He did an excellent job, and he is an honest guy.
Anyway, I picked up the bike (overjoyed) and rode it onto the street just to find out that my foot couldn't find the heel shift pedal. It was too low. I tried shifting into second gear with the front pedal but it only shifted into neutral, no further. Brought bike right back to the mechanic. He said, the only thing he did was take the gear shift pedals off, not more. He thought that when he rolled the engine back in the fork shifter (shaft shift) might have been bent. Today he told me that he took the engine completely out etc and looked at the shaft shift and it is straight. He has no explanation of what could have happened or what is wrong with the shifting mechanism. There is a distinct clunk noise when you try to shift though. Now he tells me that it is unrelated to his repair because he never touched the transmission. I can only say that I have not had any problems shifting (except for that it was a little bumpy sometimes but nothing major). I am afraid that he is gonna charge me for the repair.
Do you guys have any idea on what the problem with the shifting could be?