It all depends on what transmission you are running. If it is an E4OD, it is going to be a lot of money due to having to run a separate ECU for the transmission. Im not sure exactly what your setup is but if you can give some more details I can point you in the right direction.
Those are both for 5.0. For 5.8 you would need F5TF-12A650-BYA. You could still run one of those PCM with the 5.8 but then it would need to be tuned to run correctly. Neither of them would need to run piggy back for the E4OD as it is programmed in already (great news!). Then of course you will still have to rewire the harness. Sounds like you are close, but not quite.
Thats a lot of money but yeah, you could go that route. For 1300 though, you could do so much more for your rig (headers, y pipe, exhaust, heads, etc.). Why Mass Air with a stock 351 anyway? Mass air requires tuning just like SD so why pay so much to have it done. You could sink $5000 into a built 351 and still not need a mass air swap.
If you need a cat for smog, add one on from Magnaflow. If you live in California, you'll need two cats and I would call Magnaflow specifically to make sure you get the correct ones. They are pricey.
Then your engine upgrades..
Anything goes except for the cam. SD can not handle a cam that isn't close to stock, not even an E303. Bigger displacement and/or injectors will require tuning but same thing with Mass Air.
With the engine I'd build it like this:
351/357 cubic inches. Bump the compression to 9.5:1 if you get into the bottom end. If not fine.
convert to roller lifters (you have 94 roller ready block with flat tappet lifters)
stock 5.0 mustang roller cam
GT40 heads, edelbrock performers, twisted wedge, AFR 185's. Anything but stock heads
1.6 roller rockers, new pushrods
Edelbrock Performer truck 5.8L manifold. But check clearance in your van first!! I never had a E150
After that, you would be looking into transmission upgrades. The E4OD will handle a ton of power, but definitely not in stock form. They start to slip over 400 to the flexplate. The determining factor of how radical your engine is built, would be weather or not you want to spend thousands on upgrading the E4OD. Even before then, you will want a supercooler, tranny temp gauge, and a remote inline filter kit.