OK, so I worked all weekend and didn't have the chance to check my linkage.
Yesterday, I swapped out the bezel plate and changed over the vic. Took about 10 minutes.
I had today off, so I tried out the shifter. I can move the handle thru the gears, but it's not engaging. It just stays in 2wd.
I crawled under the jeep, and found the problem. The torque shaft has somehow slipped out of the torque shaft frame bracket. I can't be certain, but I'm pretty sure it was in the bracket when I did the swap. I think it may have popped loose when I initially tried to shift thru gears right after the swap. (The torque shaft is shorter on the 249 than the 242.)
So when I move the shifter handle, the linkage does not rotate around the torque shaft to push or pull on the tc shift lever.
It's a very simple issue, but very frustrating as well. I tried to undo the 4 screws attaching the bracket to the frame, but they are on really tight. I ended up breaking both my 1/2" and 13mm sockets. They cracked right open.
I don't think I can pry the torque shaft end back into the bracket. On closer inspection, I noticed that the bracket holder (for lack of a name that I can find) had broken. I was able to undo the 2 3/8" screws holding it on, and remove it. I also considered prying the other end of the torque shaft out of the torque shaft transfer case bracket, but wasn't sure how easy it would be to pop back in. I also considered removing the torque shaft transfer case bracket, but wasn't sure exactly how to go about it.
Here's the bracket and holder from the 242, and the broken holder from the 249. You can just see the 242 torque shaft, which appears to be about 1" longer than the 249 currently on the jeep. As well, you can see that the lip for the 249 bracket holder has broken off, leaving just the ends attached by the rubber washer.
I think I'm going to have to get a propane torch and see if I can heat up the bolts and undo them. Unless anyone can think of a quicker and easier way to fix it.
I only have cursory tools currently at hand, and no jack stands. All the good tools are up at the farm, which I don't expect to be going back to until Christmas.
EDIT: OK, after going over the shift linkage diagrams in the FSM, I think I'm going to try removing the torque shaft transfer case bracket on the otherside. If all goes well, I should then be able to attach the replacement torque shaft frame bracket holder, slide the torque shaft back inside it, and reattach the TSTCB. Sounds so easy!