MASS air conversion instructions from http://www.stangnet.com/tech/maf/massairconversion.html
A9L (5 Speed) computer from junkyard $100-$150
A9P (Auto or in a pinch, 5 Speed) computer from junkyard $100-$150
70MM MAF from 94-95 Mustang GT - $40-$70
MASS Air wiring harness kit $30-$85
The whole thing is probably less than $300 using junkyard parts.
A9L computers are 5 speed only
A9P computers are automatic, but will work with a 5 speed.
The conversion harness seems to work well for most folks. It avoids the compatibility problems in using a harness from the junkyard. Simple and cheap, actually less work that swapping the wiring harness.
Conversion Harness kits & parts
If the idea of moving & soldering wires scares you, here's a list of compatible Mass Air wiring harnesses.
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)