i doubt you screwed your syncro from a couple shifts. those things are fucking tough as shit, it really does take alot to fuck them up.... and you don't need to rebuild your entire transmisison because your 2nd syncro is fucked. also, you can replace your transmission but if you don't find the problem then it's going to happen again.

anyway, i'm almost sure that your master cylinder is fucked. try this... get someone to watch the fluid level in the clutch fluid reservoir while you push the pedal in. if the fluid raises at all, that means the fluid is bypassing the piston in the master cylinder and you need to replace it.