Do you have a spare set to experiment with?
I know for a fact that in the early days of plastic eyeglass manufacturing, sunglass lenses were tinted with good old fashioned RIT dye. The lenses were put into stainless steel tint tanks that kept the solution warm. I have been curious if this would work for the upper doors; theoretically the black fabric would be unaffected since it is "waterproof" and the clear would accept the dye. It might be difficult to get the color to match the factory rears that way however.
Your other option is to take them to a boat cavas shop and have the clear plastic replaced with tinted plastic. I inquired about this from a local place and they said it could be done fairly easily.
2002 TJ SE
2007 Rockwood Freedom 2280