It could be oil incompatibility. When you drain it down, there is always a little bit left in there, there's just no way around it. Guess what remains- the water, dirt and stuff that is heavier than the oil. The new oil has additives that suspend a certain amount of water, so what's left will mix in and eventually contaminate the new stuff. So it may take a couple of changes to get the system truly cleaned out.  As an example: my neighbor has a Deere that even though the hydraulic oil looked ok, the tractor wouldn't generate hydraulic pressure when it was below freezing. I told him to change the hydraulic oil, as any water that was suspended in the oil can form ice that will plug the filter. The fresh oil fixed the problem. 

The hydraulic filter is available, either by Oliver part # LA 5351, or you can get one at an auto parts store using Wix # 33110.

The oil leaking on the brake pedals- the PTO clutch drum is turning whenever the motor is, so if oil gets in that area it will sling it around. If you crawl under the tractor, you'll find an inspection cover that can be taken off with a 7/16 wrench. Normally this cover is taken off to adjust the PTO clutch, but when you do it, you will want a pan handy to catch the oil that comes out. You might be able to tell where the oil is coming from once the cover is off, plus it will get the oil out of an area that needs to stay dry. The only way to change the leaking seals is to split the tractor.

The seal on the bull pinion is still available. After looking at the parts breakdown, the cover that the seal is mounted in can be removed from the tractor by removing 5 nuts, making the seal easier to get to. The seal is part # E1110, and you'll also need an o-ring, part # #E1117, which is 1/8 inch thick with a 4 3/4&quot; inside diameter.

They are great old tractors, but old seals do get stiff and worn, and will leak. I've gotten to the point where I just automatically figure that all the seals on an old tractor are going to need to be replaced.