AW4 shifter positioning... Is it the same as an AX-15? What about shifter handles can I use the XJ's?
The AW4 has a cable to the shifter. You can put it anywhere you want.
You do not have to do a fuel injection swap at the same time. You could keep an AW4 happy behind a 4.2L setup or a 4.0 motor with a 4.2L setup bolted on it. The computer can be wired directly or you can use the fancy manual shifter that is available but pricey.
You can also fuel inject using the 4.0 intake but keep your 4.2L accessories. In other words you stick the AW4 flexplate on a 4.2L, stick the 4.0 Intake on the 4.2L, keep all other Vbelts, power steering, and accessories stock 4.2L. You can use the automatic cooler built into the radiator but I would suggest an aftermarket external cooler, which most guys run anyway with the stock Eagle transmission.
A MPI fuel injected 4.2L is very conservative because of the old gas sipping camshaft. You won't get high output power but you will get better fuel efficiency. My CJ8 was set up that way. It needed a special Vbelt harmonic balancer from Hesco for $350 for a Crank Position Sensor, but you won't need that because your AW4 provides the CPS.
The 4.0 intake will work with the cast iron Eagle exhaust manifold on a 4.2L or 4.0L head. The later cast iron exhaust manifolds have a built in Oxygen sensor hole that works great for fuel injection 02 sensors (just pull off the stock 2 wire sensor and put on a 4 wire version). You can also use a 4.0 header with a 4.2L intake on a 4.0L head by denting the exhaust to make room for the big intake heater. The only combination that doesn't work is a 4.2L intake with 4.0L header on a 4.2L head.