Newbie 1963 RUS with issues

So I just bought a 1963 RUS, SN 37840. It starts up and runs fine. PTO has been running and lifting a 5ft bush hog. I think this old girl has potential, but after opening up the fill holes for the transmission and hydraulic system, I realize they both have water contamination.

I'm also having trouble shifting most of the time. I have to grind and force the gear shifter into each gear. Going from 2nd to Reverse works great though. Could this be a water-in-transmission issue? Or maybe something to do with the clutch?

While under the tractor, I noticed a small hole in the bottom of the housing approximately where the clutch would be. There's a cotter pin stuck in the hole and it drips what appears to be a oil/water combo. Could this be a weep hole to drain the clutch housing? I wiggled the cotter pin around and got a big gush of fluid.

Sorry I've posted so many things in one post, but I'm slightly overwhelmed with getting started with this tractor.

The cluch area should be dry so you do have some kinda of a seal issue right there, water in the trans could cause a lot of issues, some surface rust on the gears could cause some hard shifting, When i broke into mine i did find some rust on the shaft that the gears slide on, below is a photo of my transmission on my 1964 1010RU

Ok. I got the fluid in the transmission and hydraulic system changed out today. The hydraulic system was really low. I bet I didn't get 2 quarts to drain out. I topped it off, but when I was running the tractor afterwards, there is a new high-pitched whine. It sounds like it's coming from the hydraulic pump, under the steering wheel. Why would it start to make noise when it finally has a full amount of fresh fluid? I used JD Hy-Guard, by the way.

I also have another mystery. I decided to look at the fluid levels in the final drives. (I didn't have enough oil to change it, I just wanted to top them off if they were low). I pulled the upper "fill plug" and had at least a quart of oil pour out of it. How did all that fluid get in there? I thought I might have a bad seal with some other system, but all the other systems were contaminated with water. The oil that came out of the final drive was a nice dark brown, no sign of water at all. The opposite side was full and it wasn't contaminated either.

I bush hogged for about an hour with it and it started dying on me. It would only run for a couple minutes and then it would die again. I know it's either fuel or spark. Are 1010's known for one more than the other? I've read a lot about checking the spark, but I've never actually done it. It seems complicated...

I thought I'd post a pic of my new purchase. She looks better than she is! The "wheeler-dealer" that I bought her from just had his buddy shoot a fresh coat of JD Green on the tractor and sold it to me. That paint hides a lot of issues.

I just put the 1010 decals on and I'm having the JD hood decals printed by a local company.

I'm having trouble getting the pic to upload and show up on the blog, but here's a link:

https://i.servimg.com/u/f74/18/48/45/19/deere13.jpg