I'm no expert on FE exhaust, but I found this on a Mustang site.
"Prior to Ford's introduction of the 428 Cobra Jet engine in April 1968, dual-exhaust Mustangs were only available with 2-inch diameter exhaust systems. But with the new power-plant also came new exhaust, and for the first time, 428 CJ equiped Mustangs were now available with a new 2.25-inch, better-breathing, exhaust system. And with that change, the tailpipes changed from a 2-piece, clamped-together design, to a one-piece welded-tip design. The new tailpipe design began in 1968 and carried over to 1969."
Those Cobra Jets came with some pretty sophisticated cast iron header style manifolds. So, unless your running headers and pretty low restriction (read racing) mufflers, I don't think 2.5" is a problem. Those CJ's were pretty fast with the 2.25's.