As you have noticed it is a tight fit with the JTR conversion and full length headers.. If I recall correctly, they make metion of the fitting challenges.
Anyway the Driver side Header had to be dimpled for the steering shaft to clear. The frame clearance is okay, although the control arm end is touching.
Ground clearance for the collector sits about 1 inch below the frame rail. The header tubes drop about a half inch or so below that before raising back up at the collector location just past the firewall.
Having had the Scarab conversion on another vehicle it was using the Hooker Super Comp full lenghth headers.
I still have those headers in the garage. On the driver side, the first tube is removable.. maybe to fit around the steering shaft. They hang lower (too low) and will not fit in the JTR engine location as best I can recall.
So on that vehicle after JTR setup I'm using the Hooker Super Comp block hugger headers.
There is no clearance issue with them although they are shorty headers not full length. Those are small and close to the engine and the tubes collect in center and go straight down, but not far. You just have to make a 90 degree turn toward the back with the exhaust after the header.
A buddy told me that the (short length) block hugger headers are fine until you are pushing 350+ HP, then you may be able to gain benifit from full length headers.
I don't have any experience with the MSA v8 headers.. always kinda wondered about those also.