I haven't done a TKX myself yet, but I do want to point out that it's important to know what short shaft means.
The SBF T-5 and Tremec for the 5.0 had the longest of shafts and pilot tip, then the SBF, then the big blocks.
When I did my TKO, they sold a specific FE shaft and it matched my big in/out RUG-AE2 perfectly.
With all that being said, I did a TKO (no number early one) and cutting the shaft was brainlessly easy. In a lathe, we took about .500 off the splines, then about the same off the pilot tip. I'd be hard pressed to find 5 or 600 bucks in the amount of work to do it.