pro-m's blow thru "univer" is a big joke. Even one of their own employees told me they didn't work well when I called for support once. In general, blow thru MAFs are very sensative and often require transfer function calibration. I've done several dozen, but let me tell you... the first one that I tuned took 28 dyno pulls, and even with the experience I have now they still can take 8-10 dyno pulls. Plus blowing thru usually shortens the range of the stock MAF.
On a draw thru setup, expect the stock MAF to last for about 280RWHP. A 90MM lightning MAF will last to about 400RWHP, and past that you will need a custom calibrated meter. From my own data and experiences, expect that range to decrease by about 10% in blow-thru applications.
so yes, draw thru would be best. But if you can't do draw thru don't sweat it, just don't put any bends infront of the MAF or things that would cause turbulance. The EEC will do just fine, but you will probably need a custom tune. I've used the ford EEC to support applications of around 1000HP (with 72lb injectors and injector drivers), so it's fully capable. But you need the fuel system and the right setup if you want it to run to it's full potential.
Ultimatly, I Think if your turbo kit makes any real power you will have to do some EEC tuning. It's not a big deal though, and much cheaper than FAST.
Brian