46RH rebuild?

TF-based transmissions are known to run "dirty", there will always be some amount of black or gray pasty residue in the pan after the trans has been run for a while. Like @TrailBeast said as long as there aren't any chunks or shiny metallic-looking debris in the pan and the fluid is red/pink without any burned smell then it's been running the way it's supposed to.

I wouldn't hesitate to just install the TransGo kit and run it as-is. Good idea to also install a deeper cast pan (I know stock RH/RE pans are deeper than non-OD pans but cast ones are deeper still and aid a bit in cooling) and a nice big aux trans cooler if your Jeep doesn't already have one.