I know it's a long time since these pictures were requested but here are some shots of the mating surface on the center case with (in my case, pretty severe) scoring between the ports. I know these aren't award winning quality photos but I hope you can make out the damaged area. This entire mating surface (and the similar surface where the motor contacts the center case) would need to be machined. Cost wise, I think this is a very good option although I elected to go with new parts for my rebuild.
Some "lessons learned":
1) As others have mentioned (and I missed), don't forget the washer that is likely stuck to the back of the motor when you remove it (part #39 in the parts diagram). I missed it and I can testify that you really need it.
2) Use a little grease to hold the bypass pin in place while reassembling the motor/center casing. Either that, or grow a very flexible third hand. Trust me, the grease is easier =).
3) Operate the bypass lever before you put the bottom back on the case and seal it up. If the motor separates from the casing, you're good to go. Then, if things don't work when it's back on the tractor, you know the cause is not the bypass pin or part #39.
4) Leaving out part #39 and/or the bypass pin can result in symptoms that act like hydraulic "lock" (i.e. engaging the transmission kills the engine after spinning the tires a small amount). I thought failure to purge the air would cause the engine to "freewheel" (i.e. spin without moving the wheels) but that's not what I found.
5) If you're really stuck, give Derrick a call. He's very helpful and, at the very least, he can talk you off the ledge.
