Ford 7000 seperated gearbox from diff, pto no longer works

Hi guys, I'm looking for some advice as I'm very unsure of where to proceed. I just finished putting the ford back together after replacing the gearbox. I dropped in a gearbox that was exactly the same. I ran into some issues aligning the shafts into the diff and had to raise the hydraulic lift cover. The drive shaft aligned easily enough but the PTO shaft was a bit of a pain. I put it in with the clutch on it then from the top put the band around it and aligned it into position. Everything seemed to fit. Now after putting the engine back in and every other thing the PTO does not work at all. It did before pulling the tractor apart.

I'm pretty sure that after I had aligned it and put the band around it, I was able to turn it (at the rear of the tractor by hand) when not engaged. Now after starting the tractor and driving it, it does not engage when the lever is pulled. Also a lot of heat is felt on the diff housing which implies that the clutch is slipping. Also now I can't turn the PTO by hand.

My plan of attack is to drain the hydraulic oil and raise the hydraulic lift cover again and see if I can see anything. If anyone has any advice it would be much appreciated! I will follow up with pictures after I lift the hydraulic lift cover again.

When you joined the trans to the rear axle housing, did it slip right together eventually or did you force it with the bolts? If you sucked
it up with the bolts, something bad happened, such as breaking the rear support and/or seal rings or knocking something out of alignment.
Figure on taking it back apart and spending some dollars to replace some pieces.

Initially I did attempt to pull the gearbox into the diff with bolts, having the clutch on the diff and getting the shaft into that. Eventually gave up and lifted the hydraulic cover and did it the way I wrote which did go in smoothly. That probably did it then. I'll have to seperate the diff and gearbox again. That's not a task I'm looking forward to.