Clean is good. I did degrease and power wash mine a few times before beginning the dismantle. I still found dirt and grease in behind bits and eventually won that battle. The gear cases, once open will need to have the old gaskets removed and with the covers off, flush them out. A couple of sweeps with one of those magnets with a telescopic extension will pick up most of the bits you didn't flush out. I used diesel fuel but solvent or other similar products will work. You will probably find a layer of emulsified lube oil from the water in the oil coating the bottom. A brush and a flush will get you to look like the picture I posted. I used a 5 gal bucket under the drains and let its settle out before transferring the clean diesel into another bucket for another flush. I didn't drill the drain hole in the shuttle case as my screen was not plugged and I did a complete tear down with all new gaskets. I would suggest that if you can't see the screen, its a good idea to drill the access. If you are taking it apart anyway, wait until you see what is in the bottom of the case and then decide. With the plug below the pickup screen, its would be easy to clean.
For your top covers, I would scrape off all the old gasket material and get a couple of new ones. Use a good brand gasket sealer and you won't have water issues. Silicone can be a problem if any of it ends up inside the shuttle case as a bit coming off will plug the oil channels. I tend to stay away from it in this type of application. I'm sure lots of people will tell you it would be fine but I've seen pictures of the pickup screen and some of the junk blocking it was old gasket and silicone gasket cement.
The brakes are not on the wheel axles on these tractors, so that small leak would not be an issue for now. The seal will eventually need to be replaced. Two actually, one at each end. The brakes however, are located on the outboard side of the differential shaft, ahead of the rear axles. There is a seal and O ring as part of that assembly that will leak and oil your brakes. Its a bit of a procedure to change the seal and O ring on each side but that is best left for another post after you have researched other threads on here for what to check and how to proceed. If the brakes are oiled, you will need to do the seal and O ring or all the work will be wasted in short time. Don't overfill the oil as the 17qts will get you a level around the middle of the axle, which is good for bearing and gear lubrication,