On vacuum disconnect models, the transfer case shifts into 4WD and while doing so switches vacuum to the axle to engage it. Later Cherokees of all types dispensed with the vacuum disconnect, and many people prefer this, since the vacuum setup is unreliable and can be expensive to repair. If you like the ratios, I'd say go for it. It will go in and out of 4WD just fine. Your only concern will be that the indicator light will not light unless you replace the vacuum switch in the transfer case with an electric one, or rig the vacuum switch to actuate the light directly (it is presently actuated by vacuum from a third line on the axle disconnect motor).
I'm guessing that your prospective new axles come from a model with full time 4WD, which did not have disconnecting axles. The only thing I'd be cautious about here is if it is one of the earliest V6 models that had constant velocity universals in the axle. Nothing wrong with that per se, but I think they could be expensive to repair, so if you see boots on the universals in the axle, make sure that they're in good shape.