Brake/transmission keeps turning brown/dark green color

I assume you mean the clutch reservoir fluid? From the description you likely will want to flush out the fluid system. It sounds like it may have been contaminated with oil or similar and that is causing problems. It may be too late now if it is also causing shifting issues as the slave cylinder may have seals that are starting to fail and it is bypassing fluid internally.
I would try doing a flush though, Basically you will need to get to the bleeder for the clutch, then draw out the dirty fluid from the reservoir with something like a turkey baster, fill it full of clean fluid, then open the bleeder and lightly pump the clutch, keep filling the reservoir as you do this, and keep going until the fluid out of the bleeder is the same as the clean fluid you are putting in.
If the fluid again changes color and you have shifting issues after the flush then it is likely either a bad master or slave cylinder that has internal parts that are failing.

You're welcome. Let us know the results. I would also rub some of the fluid between your fingers, you are feeling for grit in the fluid. That can be a sign of corrosion and rust in the fitting, lines and cylinders. If it is black or looks streaky that can be the rubber components breaking down.