A stock 4.0 is not
the same as a stock 5.2/5.9 (mounting wise) but can still fit
in a 4.0L with some slight modifications. However, unless you're running an electric fan or something other that will drain extra current from your battery, I would highly recommend just sticking with a stock 4.0L 90A. The biggest reason is because the amperage is different: A stock 5.2 is rated at 136A and a stock 5.9 is 150A. Unless you upgrade your battery terminals, wiring, and connectors that run to the alternator, you may not notice a big difference in the charging system, since the stock wires are not rated for that kind of current. I know they're not the greatest alternators, but I run a NAPA 90A in my 4.0L and I haven't noticed any problems yet. The voltage remains fairly constant.
However, if you do go through with the Dodge Durango alternator, make sure it's from a 5.2 Durango, and not a 4.7. Although I've never tried, I can't imagine that a 4.7 alternator will fit in a 4.0L
Hope this helped, and be sure to keep us posted