As a clutch disk wears out, the engagement point should get higher and higher. If the disk is almost gone, it might be a good idea to put a new one in there since the transmission is off. Though the problem doesn't seem like it is the clutch, sounds more like a simple engagement issue.

Did you try adjusting the master cylinder rod for more engagement ? It could even be a worn out clutch fork and pivot ball causing you to lose some throw.

Maybe the mechanic knows this and will fix the issue along with tossing in a new clutch, I dunno....