I'm not sure about your automatic transmission shifter--there must be a way to adjust the linkage so you regain those gear selections.
However, to clear a few things up, the transmission is a separate sealed case, as well as the transfer case. Because you have an automatic transmission, both the tranny and transfer case take ATF (automatic transmission fluid) as their lubricant of choice, but neither of the case share fluid in any way. Otherwise, the slip yoke in the back of the transfer case is supposed to have ATF to keep it moving with the driveshaft. The busing inside the slip yoke cone has probably loosened up, or the slip yoke on the drive shaft has worn down enough to allow the oil to flow by slowly. It's probably worth taking the cone off the back of the transfer case and replacing the bushing and the seal to make sure it fits snug.
1989 Jeep Wrangler - 4.0 swap, 32" BFG M/Ts, RC lift
1997 Acura 2.2CL
2008 Honda CBR600RR Graffiti Edition