Going to take a swing at someone adding an inch to your clutch pedal rod. I want to laugh at all of the people that get so damn concerned over this. His clutch pedal didn't come up all the way, it's not even with the brake pedal, so he cut and added an inch to it. OMG! If you don't want to modify yours again, Mega Parts has them, under trans parts and the clutch rods and components, $50.
When you get this sorted out, your pedal doesn't have to be even with the brake pedal, as long as you have separation between the pp fingers and throwout bearing. The spring between the fork and bellhousing does that. But, you have a ways to go before worrying about that one.