The bearing that supports the long shaft is part way into the Trans / Diff. housing (bearing that the cap that you took the three 3/8 bolts out of). The housings are not aligned, PTO has shifted from use. Loosen the four 1/2 bolts that hold the PTO housing to the Trans. / Diff. housing and tap the PTO housing around & shaft will come out.
Install the long shaft & bearing before tightening the four 1/2 bolts when reassembling.