Check your new clutch disk thickness. I just put a new clutch in a 35 and the new clutch disk was thinner than the old one I took out. (The old one was contaminated so I didn't want to reuse it.) The thinner disk will affect the release finger height adjustments. In my case, when I used the adjustment tool shown in the service book I ended up with quite a bit of the finger height adjustment bolts sticking out the backside of the clutch fingers and I new it would probably crash into the PTO disk rivets if I left them that way. I then looked on Big Deans CD and found the following:
"When you don't have the proper tool to set the finger bolt height Screw the bolt in till the threads are flush or 2 to 3 thread below the thickest part of the finger. Then measure from the PTO disc & set the bolts to where the top of the heads are all 3 the same height from the PTO disc After you have the clutch bolted to the flywheel and the Tee bolts removed. If the bolts stick through to far they will hit the rivets on the PTO disc causing it not to release. I have set them like this many times & the clutch work fine."
- Quoted from Big Deans CD
After adjusting the bolts using Big Deans instructions and joining the tractor back together I can feel both stages of the clutch through the pedal as expected. I will have to wait until I can start it up to see if it works correctly.