Well, your tractor is 3 times the size of my biggest tractor, a MF GC2310 SCUT TLB, which also uses the sump for the reservoir for the hydraulics. My loader GT has a totally separate system because the sump only holds enough fluid for the hydro and a few small implement lift cylinders, and not enough to also support the loader.
Being a cheap and lazy sod, and not much into re-engineering systems that have been proven to be adequate, I'd use the existing sump with a strainer and filter for the loader pump. There should already be a vent on the sump, possibly by making use of the open spaces around the shifter that you are concerned about, and more likely some other type of venting device on top of, or near the top of, the housing. The vent on car and truck differentials is a barbed fitting near the top of the pumpkin with a short hose hanging straight down. That has worked satisfactorily on rear wheel drive cars and trucks for decades. As long as the vent is made to keep out insects, water, and major debris, it doesn't really matter what it looks like. The sump contains meshing gears and bearings that are subject to wear that will deposit particles into the fluid from inside the sump where a filtered breather has no effect.
It is very easy to spend a lot of money trying to guaranty that no dirt enters the sump. Periodic fluid and filter changes that need to be done to take care of the debris created internally anyway are a lot cheaper in the long run.
If you run into an overheat problem with the hydraulics, inserting a cooler and a fan into the return line is easy enough to do.
Cleanliness is critical to hydraulic systems, but that is what the fluid filters are for. :fing32: