engine) 4.0L would be the most strait forward
fuel economy) No free lunch
towing) depends on what you're towing and what gears, I wouldn't want to tow much with an A4LD automatic, as least not with out an upgraded cooler.
cost) a vehicle is as only as cheap as the person doing the work. Hard to estimate that since there's no definite costs involved. It's as cheap as you can do it for. I guess it can vary from $10 (yes, there are people that claim this sort of total price on swaps) to a few thousand. Just depends on circumstances. I would expect a few thousand just in labor to have a shop do it, so either way....