the harness that dealt with the transmission on my 98 was all together with fuel injectors, etc. no extra transmission only harness that i remember. the manual's main body harness (that includes C101) has 2 extra wires that the auto does not have. i had repair some mouse damage, and thought i was good with an auto harness. not the case. i had to pig tail the auto harness, and then swap over the pig tailed wires that matched to the chewed manual connector, and then lengthen those extra 2. I also had an auto ecu in it from the previous owner which threw crazy codes, and the codes are how i found out i had an auto ecu.
from a thread where i asked:
"534AD is for a 4.0 with AW4 transmission.
'98 PCM 4.0 with manual transmission/Federal Emissions is 56041 531AB. With California Emissions - 56041 532AB."
the manual ECU i ended up using was a 531AF.
long story short, make it easier and get both harnesses out of the manual. the reverse switch connector should be on the harness with the injectors, water temp, etc.