. . . The Pump will not reverse from raising the trunk lid to Pulling it back down.
Sorry to hear that you haven't been able to isolate the problem, I think we're reaching the end of the easy things to check and resolve . . .
You probably realize this, but just in case someone doesn't, the pump doesn't (shouldn't) reverse direction. A solenoid inside the block shifts a valve to reverse the direction of the fluid flow. There is a possibility that a valve is stuck; due to debris, or that the solenoid isn't other wise able to move it. It might be something I would try fixing, but it would take an evening and I'd have parts spread out all over my kitchen table. (If it's a sealed unit, I think I'd raise the white flag.) Cleaning would be relatively easy, (just make sure all the parts go back in in the right direction . . . ) checking the electrical components might take a bit more ingenuity
My one last question would be if one of the limit switch leads have been swapped? But if you didn't work on them, they should be ok as is. A VOM on the leads at the pump while you trigger the limit switches would eliminate this issue. I'm not sure the system is smart enough to recover from a bad switch (position) signal.
I haven't done this so I'm guessing a bit, if the valves are driven by an electric solenoid, (probable) it might be bad or frozen. If there is debris in the valve/valve body then a disassembly and cleaning would probably resolve it. Valves can typically be 2 position or 3 position, and be driven by one or two solenoids. If it's a single solenoid valve, it might also have a spring return in which case a broken spring might also cause the problems you see.
Sorry I can't be of more help, but I think you've eliminated all the "simple" issues. Professional help or a replacement unit might be needed at this point. If someone could give you a temporary swap, that could prove very helpful. Tophydraulicsinc do say they rebuild pumps; no idea on the cost though.