I have not gotten this deep into the Kubota transmission,but reading the book on removing the PTO shows the tranmission is dis-assembled and on page 3-S50 talking about the shaft remove the internal sanp ring, then tap out the shaft to the front and the picture shows a tranmission laying on the floor.
How did you damage your PTO?
Trust this helps in making a choice whether to pay some one else or go into the learning mode. I have a 3600 and the same book is for both sizes tractors.
Friday the 13th. isn't a good day to remove transmissions. se'ya ken