Although the Mach 1 was a product of re-cycling many exiting parts, the engine was not one of them. It is not the unused dog engine that was destined to be used in the 02 Cobra. That comes directly from Scott Hoag who designed both the '01 Bullitt as well as the SN95 Mach 1. And the side scoops are standard Mustang, if you have Termi inserts, someone replaced them. The C-pillar and quarter windows were Bullitt sourced, and the seats were Cobra based. There were many unique pieces as well, but there were budget constraints which kept things like Cobra Jet scripts off the shaker.
They were not replaced. I was crossing the scoop with the insert, the Mach1 side scoops say:
TERMINATOR VT 4203
If you read Iron Fist Lead foot they mention an engine they designed that was just a tweaked improvement of the 2001 Cobra that was rejected. Why would Ford spend R&D on 2 projects to create nearly identical engines? The fact it also has Terminators heads and cams rather indicates it was created alongside the Terminator project.
If they built it separately then they should have fought for 96-98 or 99-01 Cobra cams in it instead of the Terminator cams. The fact that so many cost cutting things had to happen leads me to believe the car wasn't really intended to happen, which then makes more sense to reuse something rejected from SVT than to build another engine.
Also Cobra Jet was rejected as the SVT team objected to the use of the word Cobra, which is why they settled on the reuse of the R code. Finances made them scrap the active shaker scoop that opened at higher speeds and closed at lower. One of the prototypes for it showed up on ebay a few years back.