I dealt with this issue when I had the wrong size thrust bearing for my clutch. Sadly the size was too small to adjust it out and I had to pull the whole enchilada to swamp in the correct clutch parts.

Anyway. To adjust the nut on the pushrod, simply get an adjustable vice-grip plier and clip it on the lower end of the threaded part of the rod. Then you just adjust the outer nuts with your wrench as needed. It works fine and since you're unlikely to *ever* need to thread the nuts that far back, it won't cause any trouble to muss-up those threads. Just be absolutely sure you don't score up the smooth part of the rod or you might end up with damage to your slave cylinder seals and a non-working clutch.