The 90 is an oddball harness and needs to mate to another 90 model harness. The two odd plugs you are referencing are the source of the problem. If you had a 90 model 5.0 Mustang Ford OEM wiring diagram, you probably could move some wires around and make it work. The Ford OEM diagrams show the connector shapes and pin locations so you can move the wires and tell what's happening. The wire color and stripe are often a clue as to what the wire connects to and what the circuit is for.
Copied from bbunt302
Just for reference, here's a list of all the compatible years:
89 harness should work for 86-89 as long as you're using mass air.
90 harness will only work in a 90. (B/c of air bags and dual dash connectors)
91 through early 92 harnesses should be compatible (single dash connector, fuel pump relay under driver's seat)
Late 92 through 93 harnesses should be compatible (single dash connector, fuel pump relay under the hood)
AutoZone wiring diagrams
For 79-88 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c1528004e28c
For 89-93 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c15280069677
For 94-98 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c152801f5e3b
For 1999-2005 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c152801ef7d7
Larger MAF to go with Mass Air conversion:
94-95 Mustang GT MAF - $40-$100. It is 70 MM instead of the stock 55 MM on regular stangs built prior to 94. It uses a slip on duct on the side that goes to the throttle body and a 4 bolt flange on the other. You need a flange adapter to fit the stock slip on air ducting that goes to the air box. Wiring plugs right in with no changes. *1 *2
*1.) Metal flange adapter http://www.kustomz.com/cat3.html Buy the TR70 for $44.95. Or spend some time on eBay looking for one that may fit.
Try AutoZone and ask for 81413 - Spectre / 3 in. Aluminum Intake Mass Air Flow Sensor Adapter at $12.00. You may have to order it online.
*2.) MAF & sensor interchange
The 94-95 Mustang 5.0 MAF & sensor is also found on:
1995-94 Mustang 3.8L F2VF-12B579-A2A,
1994-92 Crown Victoria 4.6L F2VF-12B579-A2A,
1995-94 Mustang, Mustang Cobra 5.0L F2VF-12B579-A2A,
1994-92 Town Car 4.6L F2VF-12B579-A2A,
1994-92 Grand Marquis 4.6L F2VF-12B579-A2A,
Evidently the –A1A, -A2A, AA, etc. on the end of the part number is a minor variant that did not change the operating specs. You should be able to ignore it and have everything work good.