Did you use the 216 bellhousing or one from the 235? The clutch fork and throwout arm may not match. You should be able to get it all to work pretty easily, though, I am running a '62 261 with an 11" clutch and flywheel with a 216 bellhousing. I just had to dig around to find the right release bearing to let the clutch engage all the way. It seems my pressure plate is pretty tall.
You can safely run the engine with the sheet metal shell on the bottom of the bellhousing removed. You should be able to have someone step on the clutch (with the engine off) to see if the release arm is pushing on the throwout bearing and the pressure plate springs are moving. If they are, you may have installed the disc backwards.
