Limp mode, codes U0101, P1603, P1604, 0037, 0031

Car has been sitting because it was in having intermittent stuttering. I remember seeing PCM codes although I cannot remember them. Fast forward about two years later I start working on it. Starts and drives okay. Every other drive it wont shift into overdrive and running rough. Changed ATF4. Car wont shift out of second now. Changed input/output sensors, and crank and cam. Car runs better but still stuck in second and no speedometer. Scan gives u0101, p1603, p1604, and 0037, 0031. I began thoroughly inspecting harness and connectors. However looking at C1 PCM connector I am not sure if pin 13 is supposed to have a female copper to marry up with pin. I see it as vehicle speed signal on schematics but I cannot find anything to verify if there needs to be a copper piece there. I also didn't make it to the scrapyard before it closed to check on a different one. Picture I will send. Thanks