Here's a quick list of things all new D2 owners should be aware of and have checked.
Front driveshaft - the stock unit does not have zerks to lube the u-joints. The slip shaft is there, but nothing on the caps or cross of the uj itself. This needs to be replaced with a serviceable shaft ASAP. You can get one from Tom Wood, or search for 1300 series u-joints. The TW options bumps the size up to 1310's. If the d/s isn't serviced, or makes a vibration at speed, there's a good chance it will seize, break, and knock a hole into your transmission.
3 Amigos/ABS modulator - Sometimes the ABS line connection in the wheel well goes bad. Sometimes it's the modulator itself. It can also be caused by dusty pads and squealing of the brakes. In either case, the 3 Amigos (ABS, HDC, and TC lights on the dashboard) is something all D2 owners get to experience at some point. There is a cheaper rebuild kit that sometimes works.
Rotoflex coupler - This connects the rear driveshaft to the flange of the diff. Time, and or a lift can cause this to crack and eventually fail. Inspect your current one. If it's not too bad, get a new one and keep the old as a spare. Better yet, get the 4 bolt flange off a D1 and you can use drivehafts from Tom Wood.
CDL - Here's the breakdown of the CDL guts in the transfer case by year.
1999 - mid year 2001, CDL is in the t-case but not connected to the lever. You need to crawl under with a 10mm wrench and do a 1/4 turn to lock it. Reverse to unlock, but beware of the hot exhaust.
Later 2001 - 2003, No CDL at all in the t-case. You only have Traction Control
2004, CDL in the t-case with a cable connected to the lever.
I installed the '04 shifter into my 2001, which has the CDL guts in it. To check if you have it, feel above the front output flange. It might be easier to take a picture to do this. You can also install the linkage from any D1, but there is a bend you need to make for it to clear. Most of them are never used and need a bit of penetrating oil to free the linkage.