Matt,
Although I would expect your transmission would be leaking without sealant, I'm assuming the pics are after you removed the sealant from the mating surfaces of the transmission and transmission cover. When replacing the cover, make sure the sealant has plenty of time to cure before adding the hydraulic fluid or you wil risk having leaks...I had to let the RTV sealant set for 24hrs.
Other than pulling the PTO Clutch and PTO Clutch brake shoe / piston out of the transmission, I haven't been any deeper into the transmission. I can't remember if there were any other seals / O-rings in the PTO clutch assembly or not. Since your transmission cover doesn't have the "fingers" to hold the oval O-ring in place, you are going to want to use a paper clip to insure the oval O-ring stays on the seats while you put the cover back on and tighten the bolts. I was pretty sure a deformed oval O-ring was your problem, so I'm pretty much at a loss now, however, replacing the two O-rings could still do the trick.
A word of caution when reinstalling the rear PTO cover. You may find that the cover aligning studs may not fully align without exerting force on the cover (from left to right as viewed from the rear). This is due to the PTO brake compression springs. Even though the Deere folks say it is OK to gently pry the cover with a screwdriver, I would not do that....at least one member here cracked the rear cover doing so. The best thing is to partially remove the PTO brake inspection cover on the upper right rear to release the pressure applied by the 3 concentric PTO brake springs. (I assume you removed the cover entirely in order to change the PTO brake O-ring).
Also, if you want to know if the PTO solenoid is working, you could remove the PTO brake cover, remove the two smaller springs and then replace the cover (when doing so, insure the PTO brake shoe piston stays firmly in place to insure the brake shoe doesn't fall off). This should remove enough brake pressure against the PTO clutch to allow the 50lbs of pressure you do have to drive the PTO clutch under no load. Don't forget to put the two springs back once you are done.
I'm hoping the O-rings do the trick...otherwise you are blazing new territory here.
TimF