2 MAF pigtails on wire harness

[240roadrace]

I recently replaced the main engine harness on s13 KA24DE. The old one had bad wires on TCS and MAF was cut and spliced.
New harness has correct 4 pin connector where MAF pigtail should be, but also has a short 3 pin MAF connector right by valve cover, where TCS, TPS and ground wires are at(which would put MAF right at throttle body). The wiring looks OEM, not spliced in. Anyone familiar with a dual MAF pigtail configuration?
I have both 3 and 4 pin MAFs. I have tried both at the same time, and both by themselves and all 3 situations put car into limp mode and give the MAF code on the ECU diagnostic. Made sure both have ground wire connected, used MAF cleaner on both and have reset the ECU a few times. I guess both MAFs could be bad. We originally thought it was the MAF, but were not sure if it was harness or MAF.
SO, before getting another MAF, I wanted to know if it would need both(which I have not seen before), or if leaving the short one unplugged would be a problem. Or is the short 3 pin pigtail go to something else? If fits the MAF perfectlly!
Any help would be greatly appreciated.

[PapaSmurf2k3]

Do you have any pictures?
Where did you get the wiring harness from?

[240roadrace]

Harness was pulled from local pick-n- pull. My buddy pulled that part of harness, but neither of us recall what that went to or it having 2 MAFs. The short 3 pin pigtail looks dirty where the retainer clip would have been. Our MAF is relocated, but it was just loosened from harness & re-taped, not spliced. Harness was pulled from fastback, while ours is a coupe. I know it makes a difference on main interior harness, but have not seen anything about difference on engine harnesses. I've never posted photos to a forum before, hope this works!
http://s1371.photobucket.com/user/Kwyji ... s/library/