Fuel pump assy: Both setups are returnless, and run at the same pressure. Therefor, the fuel pump already in the truck will work fine. It is a good time to replace your fuel filter though, its in the drivers side frame rail next to the transmission.
Factory MAF's being calibrated to injector sizes is a common myth. The calibration is actually in the ECU. Aftermarket MAF's for large injectors are just tricking the computer into seeing less airflow, therefor opening the larger injectors less. In theory this keeps the A/F ratio the same, but a custom tune is a much better option.
That being said, the MAF's may be different due to air flow requirements, so use the OHV one to be safe.
PATS: Switching the modules is the easy part. However, the trick is getting a key with the correct code to match the module you swap in. If you move the whole steering column over from the donor vehicle, your door locks won't match. Fixable, but much more work. Another option is to get keys made that are cut to your current column, but with the chip programmed to the new frequency.
EASY WAY OUT: Simply tape the key from the donor truck inside your steering column after swapping the module over. This effectively disables PATS, as the key is always present, but is the quick and easy solution.
Chips: None of the chips or modules are worth the money, some can even damage your vehicle. If you want the best performance, get a tune from Henson Performance. Honestly though, its not really worth it on a completely stock motor. It still won't keep up with a healthy SOHC.
I think that covers most of it.
Chris