Please forgive the lateness of my reply, i am not on as often as i would like.
Its not hard at all, just like replacing a transmission or any other part, except this time your adding a little more. Disconnect the front and rear driveshafts from the transfer case. Support the transmission with a jack, remove the transmission cross member and mount. Lower the jack slightly so you can access all the nuts holding the transfer case to the tail housing of the transmission. Then just remove the transfer case. Reinstall the manual case in the reverse order.
Depending on whether you have an auto or manual transmission will dictate which shifter you need to buy, the shifter itself may be the same, but the bracket that bolts to the tail housing is a little different auto to 5-speed. To do it to where it looks right, you will need to remove your front seats, and console (if a Navajo has a console like the explorer) and pull the carpet back exposing the floor plate (silvery looking piece screwed to the floor on top of the transmission tunnel). Remove it, install the shifter, measure the shifter location to cut a whole in the floor plate, cut plate, drill holes for shifter boot, cut carpet for shifter, reinstall all parts, install shifter boot and trim. I know its a long process, but well worth it. Some of this will be different if you have a manual like I do. You will need to find a double manual shift bezel, and just put both shift boots in it. If you have a manual, you dont need to remove the seats and all, just trim the carpet and floor plate like I did after pulling the transmission shifter boot up.