Non-A-body 46re q’s

Sorry for the non A-body trans question but hopefully the very best Mopar forum will provide some answers.

I have a 1998 Jeep Grand Cherokee 5.9 Limited. It has a 46re in it that is performing poorly and making noise.

Just a few simple questions I’d like to ask for when I eventually go to a shop to have it rebuilt or buy a crate.

It’s a 4x4 so if I order one I assume it will need to be from a 4x4. Is this the case?

I have also heard about some upgrades you can do with 47/48re parts. Anyone know what parts those are? The Jeep forums don’t specify.

Thanks in advance.