wjschill,
When you say there is a "difference in color", could you elaborate on that just a bit. Are you talking interior or exterior. If the latter, does one have full body paint and the other doesn't? Or do both have full body paint, or does neither have full body paint and only decals?
I'd one has full body paint and the other doesn't, I'd go with the one with the full body paint.
As for the engines, I think that's a wash. BUT...I WOULD have a preference for the Workhorse because of the Allison transmission.
If the floorplans are identical, I guess if one of them was in a more preferential color scheme, that could be important as well. Also, check the quality of the cabinets. When we ordered our rig, we opted for a rather pricey cabinetry upgrade ($4,000ish) over the basic cabinets. The quality of these are MUCH better than the stock cabinets and I believe that was an important upgrade for us as the cabinets have really withstood the test of time. Heck, the cabinets in our motorhome are actually better built than the ones we have in our house!!! LOL
Tough call to make as I think a lot will have to do with which one looks better for you, all other things being equal.
As others have said, pulling around a 2,800 pound TOAD shouldn't be much of a problem with the proper towing gear. Both Ford and Workhorse require an auxiliary braking system, so that's a wash as well.
I think it's kind of neat that you were able to find two mostly identical rigs just on different chassis's. :)
Good Luck,
~Rick