well muddy fluid can mean many things
generally if its just dark then you just change it and clean the sump screen and change the filter.
Now if its muddy as in dark brown and exceptionally thick or has visible material in it then you have bigger problems usually pertaining the clutch packs. Now the sump screen is generally located in the lower hose outlet on the base of the transmission. It will be part of the fitting that the hose attaches to. You will have to drain fluid, remove hose and if fitting is removable by either bolts or just unscrewing remove that and there should be a screen in or attached to it. Usually if this is clogged it will cause travel issues but usually in both directions as it is not picking transferring fluid properly and can cause air to get in the line.

Now what i would do once you clean that
get a pressure guage and check
-the clutch pressure
-main pump pressure
-fwd and rev clutch pressures

if these pressures are too low you'll have found your problem.
Being that it comes and goes its hard to say what it may be.

as for testing ports and pressures you'll have to revert to the service manual for these.

good luck