I hear the MAF PCM would work for something like his app, but haven't tried it on a turbo application myself. The MS itself is a little more than the MAF conversion, but you have more control. Might be difficult getting it all configured, I might get the stock engine running good on it first before throwing on a turbo.
You'll have to completely rewire the engine with a MS, or I believe there might be an aftermarket device that allows the 60 pin Ford harness to hook up to the MS. For MAF conversion, only need to go through the wiring (make change if needed), add 2 pins to the computer harness, find a MAS, and wire it up.
My MAF computer was $80, pins/wiring/plug free from 5.0L HO wiring harness, $35 for a new MAS, + other small electrical stuff. You'll want EVTMs from Helm Inc. too (or have Ford make you copies of the same thing at the dealership).
If you went the MAF route, I would advise you to at least get an air/fuel ratio gauge for the o2 sensor so you know if you're leaning it out (so you don't accidentially fry it).
Only reason that I might consider an MS is because it can work with just about anything. When the 2.9L is done, you can use the computer on something else.
Pete