The AW4 alone would be a headache to install for the overall lack of benefits in it's standalone form. You'd need, at the very least, the wiring harness portions and the transmission controller, which would have to be spliced out from the harness and looped into the Eagle's wiring (mainly power). Flexplate and starter to match.
To add to that you'd also need the shifter since it's a cable shift transmission in it's stock form, or buy an adapter. The shifter and it's plates will fit into the Eagle's shifter hole when you swap though, and it's not too hard to find a place to slide the cable. Would have to weld on a small piece of metal to close the gap around the shifter.
The fitment of the driveshafts is another concern. If you stick with the Eagle's 4x4 transfercase you'll need a clocking ring, as well as either get your driveshaft cut for the rear or find one that fits. The AW4 is a few inches longer than the 998, it'll compress the driveshaft all the way. Best bet would be to get the Eagle rear driveshaft cut to remove about 4 inches. The front driveshaft would need to be a few inches longer, I image a Grand Cherokee driveshaft would work.
I may add that since the AW4 would move the transfer case back a bit, it may end up hitting the butt end of the tunnel so you'd have to cut a part out for fitment, and the transmission mount would have to be custom made since they don't line up. I'd toss in a NP231 t-case.
To be absolutely honest, you'd be better off passing that by. If you want more power the headswap is a solid all around upgrade to start with. Or find a 727 (swaps directly with the 998 and is heavy duty), or regear the axles.
Why do I say this? Because I'm in the middle of a full drivetrain swap and I see it all now.
My vote? Stay away from the swap unless you have the time, money and know how.
If I were to do it over? Head swap -> fuel injection -> better gearing