Just taking a stab here, but from my experience, a LOW input means a short somewhere, as a high input occurs when the sensor is unplugged.
Which harness did you replace? the ACTUAL front wiring, (including the Fuse Box & PCM plugs) or the engine side of the harness?
Also, it could very well be your VEC-2, as the VEC-1 & 2 alter the MAP signal.
May be worth your while to get a manual if you dont have one, get a continuity tester, and pull the FAR LEFT PCM plug, and check continuity of the wiring from the PCM plug to the sensor connector. (the pin output w/wire colors is in the "connector pinout" section, 8W-80-40).
EDIT- had a couple extra minutes. On C1 PCM plug, (far left), the DG/RD wire is Pin-27, the BK/LB wire is Pin-4, and the OR wire is Pin-17. Check continuity from those pins to the MAP sensor connector.
Lastly, I am not positive how the VEC-2 connects, but if it connects IN SERIES with the DG/RD wire like the VEC-1 did, you have to take a sewing needle, and push it into the insulation on the HARNESS side of the wiring, and check continiuity from that rather than the Pin, as the VEC systems will block a continuity tester, so you have to bypass. may want to check continuity over the VEC connections as well...they could be your problem too.