made some progress today, clutch and starter are in
also ran into the first problem but i may have a solutuion...
the trans harness connectors from both trucks are different, the auto is the bigger one, plan is to leave about 3-4 inches of wire from the autos connector and cut the harness from the connector, then cut the connector off the manual trans harness and match each wire from the manual trans to the auto trans harness connector, they are all there i checked, idk if it will work but i would think it would
pic of the different harnesses