I loosened the steering shaft up from inside the car and moved it over just a bit, but the header is still hitting the shaft. It does not appear to be hitting the rag joint.. Would the MM shaft fix this? In the mean time I guess I'll install my stock headers and wait for the shaft to come in ...
As
NikwoaC said, it takes a very little tap to clearance the headers. It won't effect performance. But, I can see the desire not to do that. Also, the header is close to the engine. And, you do have to clearance the header enough so
when the engine rocks, it won't hit the steering shaft.
Plus,
any Fox that still has the OEM steering shaft and rag joint is on borrowed time. So, putting in the MM steering shaft isn't a bad idea.
Yes, a MM steering shaft should give you the required clearance. But, I don't know with a 4-eye. 4-eye's have a slightly different front suspension. So, just because the same combo may work on an 97-93 Stang, there may still be some interference. I don't know if they kept the steering wheel in the same exact place when Ford when to the newer dash. A 1/4" isn't that noticeable for people doing a dash swap. But, a 1/4" is the difference between having clearance and not for the steering shaft.
You will get more clearance with the MM steering shaft. You cam call/email the people at MM (very nice and knowledgeable) and ask if they know how much more clearance their steering shaft provides. IMHO, email would be best for a very specific question like that.
If you do replace the steering shaft. Make sure you have the steering wheel straight and the wheel straight. When you put the steering shaft back on, make sure the steering wheel didn't move at all.
I forget, but I think that the stock steering shaft has a ?torx? or weird bolt at the end ner the rack.
Also, it's a PITA to get to the bolt and nut near the firewall. Two people would be great. Doing by yourself really sucks.
IMHO, I'd "clearance" a header before I went through that hassle again.

But, you do get more precise steering (and more road feel - some see that as bad) with the MM steering shaft. And, you won't have to worry about
when your rag joint will go.
So, there are you options. Your choice. I only push people away from getting screwed by companies and doing bad/risky things. Otherwise, it's up to the person to decide what's best for
their desires and needs.
Good Luck!