Allis chalmers 6140 hydraulic issue

So i got a 6140 with the 4x4 option. Its got pretty low hours. However the former owner got water into the universal tractor fliud which is shared with the transmission and hydraulics. Naturally i drained it, replaced the intake filter and afterwards i began having issues with the lift arms not lifting as they should (lifting whenever they felt like and only for a few seconds, with no rhyme or reason). So i bought another pump. By the way a krp4-23cssbkd pump for a toyota forklift will fit this tractor, but you have to cut the length of the inlet pipe about .380 (if memory serves me correct) shorter to match the inlet bolt holes on the pump. I just cut a section out and sleeved it with automotive radiator hose. While after the pump change it appeared the lift arms were working better, they still are working intermittently and even when i activate the remotes it doesnt seem to be bogging down the tractor like it should. So im scratching my head. Im considering changing the fluid again (honestly it could use it) to get the rest of the crap out as well as tbe filter. Im no expert on hydraulics so this is new territory for me. I did take the pressure valve apart beside the remotes and cleaned it out. Nothing in it looked visibly wrong. Any advice?

I had one with similar issues, I sent you my number in a pm, give me a call

Big thanks to ben (brouilletefarms) for tbe insight. We talked on the phone and suggested it may be do to clogging from the wet brakes deteriorating after there was water in The oil. Im going to check that. Tribco in ohio sells brakes for this tractor ($76 a brake, ouch!) So theres at least that.