depending how crazy you went with your stroker, the NSG370 isn't likely to be happy with the combination of the increased power of the stroker and the increased weight of a full size jeep. Chrysler rated the NSG370 for 272 ft-lbs of torque, and really only put them in wranglers and liberties, none of which come close to the weight of an SJ.
If you're planning on wheeling it and have big tires, I'd be looking at other transmission options myself. The NV3500 was rated at 300 ft-lbs which has a bit more of a cushion, then there's bigger truck transmissions which will certainly work better off road. Don't underestimate the power these strokers make down low, it's a mistake I made in a much lighter vehicle recently
If you're not planning on wheeling it much, I could see why you'd want the nicer shifting NSG over the NV3500 (or even the NV4500).
To answer your question about fitment, though, the jeep 208 and the NV241 were the same input splines, diameter, and pattern, so it should bolt up as long as the input splines are the same. The NV3500 will use the same pattern as well. If you wanted to keep mechanical linkage, advance adapters sells NV3500 kits to the early bronco crowd that keeps the mechanical linkage.