Big engines and FMXs can work just fine
Here's a pic of a 71 Mach 1 with its original FMX, but it now has a 484-inch stroker in front of it.
http://www.mercurycougar.net/gallery/showphoto.php?photo=727&papass=&sort=1&thecat=500
The car was originally a 351C-2V/FMX/2.75 geared 9". It is now a 484/FMX/4.11 geared 9". We used the bellhousing from a 351M/FMX that was in my old light duty 78 full size LTD wagon.
This car runs 10.90s-11.00s. He's running the FMX because 'they' said it shouldn't be done. It has only been rebuilt once, when he made the mistake of a starting line launch in 2nd gear. Only one rebuild in the past 30 years isn't doing too bad, eh? Other than that, it has just a plain old shift kit and high stall converter. The aftermarket places still have high stall converters for FMXs, they just don't advertize them since the market isn't there.
The FMX is stronger and will take more abuse than a C4. The clutches are bigger and the case won't twist or warp like C4s are prone to do. The internals of the FMX have a center support bearing like the GM TH400. It is the only Ford trans that has one. That means that the internals will stay in alignment better and won't get twisted out of shape.
Yes, the downside of the FMX is that the aftermarket parts availability is not as good as the C4 or C6. You can't get any real hard-core racing parts for them. You can't get a trans brake for them.
But, you really don't need them either!