Great write up! I would really like to see a write up done for more advanced forms of power gain (Supercharge/Turbo) most people understand that these components are "bolt on", with the catch of having to upgrade engine components to support these changes. I would like to know how/why these changes need to made to the engine. If someone had a write up like that, it would be great.
I am not all that familiar with the Mach 1, however #2 is true for any factory tune on any mass-production car, and #3 if the stock 3.55's don't do it for you. Installing an aftermarket catted X-pipe and mufflers will likely help it breath better as well. I do not believe the intake on the n/a 4V suffers from the same issue as that on the PI 2V engines.
When Ford introduced the PI engine, raising output from 225 fwHP to 260, they used the same upper plenum as was used on the non-PI engines. Though adequate to meet the 260 fwHP claim it makes the engine fall flat after the peak output--that extra bit of air flow provided by the aftermarket designs let's it pull right up the the rev-limiter.
Similarly they carried over the 19 lb/h injectors from the non-PI engines, however they corrected that in the late 2002 production.