If it doesn't shift correctly when you manually change gears, than there is definitely something wrong internally with the transmission. Manually shifting through the gears completely bypasses the ECU/solenoids for 1/2/3 shifts (purely mechanical). No need to inspect the wiring harness or anything else at this point. If it doesn't shift correctly when done manually, than something internally is wrong. If you take a look at the FSM, it is one of the first tests it has you do in determining the cause of shifting problems. Once you do that test (manual shifting) and it still doesn't shift correctly, the FSM pretty much says you're screwed (transmission service required, or transmission replacement required, something to that effect).
That is how I knew my pink milk shaked tranny was finally toast. I also put new solenoids in it before properly diagnosing it which was a mistake (I guess I have a spare set of solenoids now though).
I was doing all sorts of crazy things like swapping ECM's, pulling the gauge cluster like Charlie suggested and so on. If I just followed the FSM test procedures in order, it would have saved me a bunch of time and effort.
What did the inside of the pan look like? Any excessive metal? How was the filter?