Well... I too would change out the MAM and injectors (and, it would make sense to do the TB at the same time, but... $$$)... and, as things go, you'll need to address the fuel pump too. In my experience, once you get around 230hp at the wheels the stock pump is done.
As far as the MAM goes, "worth it?" ... Back in the day when my engine was stock, I picked up a solid 1/10th at the track. That's about 8hp, and that was with stock intake/heads etc etc, so, you should see more than that with nothing other than a MAM swap. Worth it? Only you can answer that.
MAM, Explorer/Cobra/aftermarket, doesn't matter at the emissions house... as long as your readings are within the limits they don't care what is under the hood. They do not "look" for any emissions "certifications" or whatnot. They do look for things that are not connected... aka vacuum pump with no belt to it, EGR port cap'd off... that kind of stuff.
I like C'n'L meters... they use the stock Ford electronics. There is a well known tuner here in the valley that will not work with ProM... to each their own I guess.
ProM does have an outstanding rep, so, not saying it would be a mistake... pick one and run with it, Keith (AZDyno) works with them all.