Both harnesses should be for manuals. The engine harness should be for the '91 KA24DE DOHC. and the body harness SHOULD be for a '89 SOHC.
I haven't gotten to drive it yet seeing as how we've been having some engine trouble (see
zerothread/186639) so I can't tell you if the transmission is working top notch, but we connected all the harnesses to the transmission.
Thanks a lot man. good to see someone with some knowledge around here.