The harness would work with 6v or 12v. I've never personally changed a 6v vehicle to 12v, but from what I've read it's pretty simple. If I remember correctly you would need to change the headlights, and the bulbs for the rest of the lighting, to bulbs meant for 12v. This includes the bulbs for the gauge cluster and the dome. The gauges are also meant for 6v. The speedo and ammeter will work fine with 12v, but the oil, temp, and fuel gauges would need voltage reducers to be used. They need about 5.5v. A lot of people just install aftermarket gauges and leave those three unwired. The last thing I would look into is the coil. Not sure what would be needed there. Different coil? Ballast resister? Maybe a voltage reducer like what's used for gauges would work? Hopefully someone here will chime in and set me straight
Im pretty sure you would need 12v to run a new stereo.
In my first reply I said Cherokee axles would work fine in your wagon. A few nights later I woke up in the middle of the night and that was on my mind. I realized I had assumed you would be aware of all things that needed to be considered(except for the brakes for some reason), and I felt I needed to address them. I fell back asleep and forgot, until now.
-Stock Wagons came with d18 transfer cases which have outputs both front and rear on the passenger side of the vehicle. Cherokee rear axles have a centered pinion, and the front is on the driver side. I don't know why I didn't address those, and I apologize. You could change tranny/t-case or just t-case to run them, but watch out, cause adapters can be very expensive.
-Second thing to note is the change in lug pattern. Stock willys is 5 on 5.5. Stock cherokee is 5 on 4.5.
-the Cherokee axles also will have different gear ratios. Stock wagons I believe only had 4.27:1 and lower (higher numerically)gearing. I think most Cherokees came with 3.07:1 or 3.55:1 axle gearing. The 3.55s might work fine. Not sure you'd wanna go as high as 3.07.
-Spring perches would also need to be changed. The stock cherokee suspension mounts would need to be cut off and new spring perches welded on properly for your wagon. The lower shock mounts too.
Sorry again for not being more thorough. Hope I didn't cause any problems.
Edit- forgot to mention the stock generator would need swapped out also. A new single wire alternator would be a nice replacement.