B gears grinding after rebuild

I finally got my B back together over the weekend after a rebuild and it starts and runs great in neutral. Last night I went to drive it out of the garage and it grinds in every gear with the pedal depressed. When I have the pedal fully depressed it even sounds like it lugs the engine down a little bit.

I put in a new pilot bushing, new clutch disc, new pressure plate, and new throw out bearing during the rebuild. I made sure the clutch disc was orientated the right way when installed and used a clutch alignment tool to make sure things were centered. I had adjusted the clutch pedal free play to about an inch and a half. Greased the throwout bearing. The surface of the flywheel was cleaned up a little bit when it was at the machine shop. So I am stumped as to why the transmission shaft is not releasing from the engine. I have done some looking in the site archives on this issue, but would like some input on what the culprit might be before I go any further. I am not a clutch expert by any means.

New pilot bushing might be tight on input shaft pilot end..

Your clutch is definetely NOT releasing, could be pilot bearing like Dieseltech says, could be one finger of the pressure plate not adjusted properly and not releasing. I really doubt Rockford Clutch Division of BORG-Warner is building clutches for Case-IH.
I'd split the tractor and look every part over very closely.

The statement you made I finally got implies that there was a time lag between putting things together part way, and final start up. The clutch disk assembles with the thick part of the hub to the rear, away from the flywheel. You indicate it is correct. so I assume some other thing is wrong. Here are Three possible items. #1- the clutch disk was subjected to enough time and condensation moisture that it has lightly rusted to the flywheel. #2- The act of mating the engine to the torque tube (clutch/cover housing) was a bit rough and may have warped the disk from alignment stress. The warped disk drags on both PP and FW even when the pedal is depressed well. #3- The splines on the clutch shaft are worn from years of use. This can cause the new clutch to catch i=on the step in the splines holding the disk against the FW.
The free play should be checked, I don't think it is that large.
If the tractor can be positioned to be operated safely in an unobstructed area, aim it for open spaces and start it in 3rd gear with the clutch down (( be prepared for it to move immediately)), and shut it off if needed. Driving it around can free up the disk if stuck.
If it does not free up, it will likely need to be split to assess the issues. Jim

Did you use a bushing driver when installing the pilot bushing as and burr on that bushing will cause the pilot shaft to not stop when depressing the clutch you will need to split the tractor and fix that