[89 Cobra LX]

I would finish off the exhaust first, but I would start with headers. I'm not sure why you're against aftermarket headers, but they are dollar for dollar one of the better mods that can be done to a stock 5.0 and they certainly won't hurt the motor. You're headers will ultimately take more advantage of the MAF and T-body you're going to add. And yes, the MAF and T-body should be upgraded. Don't go bigger than 65mm for the T-body on a stock 5.0.

For a point of reference, I added a 73mm MAF after I had all of the exhaust finished and there was a definate seat of the pants difference in perfomance... especially in the upper-rpms.