Whichever decision you make, use a 1350 series pinion yoke on the rearend. Why? Mopar pinion yokes use small 1/4" bolts. More than one drag car customer or mine has come back with a damaged shaft after I told them to step up to 1350 series. If a 9" Ford is to be used, buy an aftermarket pinion support as suggested previously and again a 1350 series pinion yoke. Aftermarket parts for 9" Fords are relatively cheap and very easy to find.
If you're puttin' a 9" in a digger I recomend that you thouroughly evaluate WHICH 9" housing you use. The heavy duty housing was actually painful on my legs due to the relatively sharp corner on the edge. Sitting in the lanes could become very annoying. On mine I ended up tossing the heavy duty housing and using the medium duty housing instead - it was MUCH more comfortable. I'm gonna bet that's one of the major reasons why the 8-3/4" rear was so popular in the FED's they gotta be one of the smallest "good" rears out there. It's hard to approach the availability in aftermarket parts that the 9" has - so for me I decided 9" was the way to go. Whichever way you decide to go - you may want to consider tying the front and rear flanges of the housing together. The neatest way I have seen to do that was to bore four holes through the housing directly on teh mtg holes and weld a sleeve in. The other way is to simply weld in a tab internally. Might be overkill for a digger, but since you're sittin' on it - it might not hurt to add a little "extra"
I personally use 9" 31 splines. Escpecially for what your doing. Easier for me to swap out gear sets in about 30 minutes. So I can cruise go to 1/4 or 1/8 mile track and run any. Parts and axles are not that expensive for 9s they are easy to get. Id even consider a 33 or 35 spline application it will not break and the parts are pretty much the same cost as a 31 spline but the longevity is better.