The best way to tell your engagment height is to do the bleed first. With air in the system, you will have alot off foot action and less slave cylinder response. So if your in neutral, put your clutch pedel to the floor and the slave cylinder is moving the shift fork/ pressure plate just enough to clear the disc and allow you to get into gear, when you release there will still be little action at the pressure plate that your engagment will seem low on the pedel.

If your clutch was going then you would be slipping and getting the nasty clutch stank when it happens etc. You say it holds fine till 9k rpm so I wouldnt be so concerned about that just yet. A bottle of DOT 3 is a couple of bucks and the bleed/ flush is free if you DIY or whatever labor your shop charges. Its the starting point since you had empty reservoir. A clutch job can cost mucho $ for parts and labor so that can wait until you confirm any problems with the clutch. Let us know the outcome!
CHad

 

for Good info, im currently having the same issue