Unless your 88 is a California car it shouldn't be mass air. I wouldn't change the harness myself. Just put the motor in and plug into the OE harness in the car.
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just a side note, you can seperate and sell the MAF conversion to someone who needs it, and the density harness would be perfect for someone who wants to convert a carb'd car to megasquirt! and your keeping your cars wiring intact, instead of bastardizing it.
replaced the 93'ish coupe with a 64 falcon hardtop, 393, 11.5:1, TEA CNC 205 TW's, custom Hyd Roller, Super Vic, 830 HP, C4.