Jayhawk RV, welcome to TBN! I'm sorry you are coming here because of a problem, but we will try to help.
Your hydraulic fluid being brown is really a "red flag." It is saying the fluid has been really hot and is now cooking. That could be because of the main hydraulic system, but most likely the HST transmission as you suggested. The hst fluid is supposed to be pumped through the HST filter (small one of the left of the engine) and then go through the cooler at the front. I'd check all these lines to make sure they are not kinked and that fluid is flowing properly. The HST transmission has a small pump on the front that is called a charge pump. It pulls the fluid from the reservoir and pumps it through the HST filter and cooler before supplying cool fluid to the HST main transmission pump. If the fluid was starving or hot, it could cause HST failure. That could be the reason the fluid is dark and has lots of air bubbles.
One other thing to check (with the engine off) is the operation of your HST pedals. Have someone observe the shaft going into the transmission while you operate the pedals and see that it is not broken. Some of the early tractors had problems where the shaft broke off right at the input to the transmission and no matter where you put the HST pedals, that input was not going to the transmission. It's a bit hard to see, so a good flashlight would help to see the shaft operating.
