I took a look at the wiring diagrams (for the instrument cluster at least) & compared 1999 to 2001 - I didn't see any difference. Every plug & pin is identical which makes me think they should be compatible at least for the IC circuitry according to the WDs. But, I haven't ever been involved directly in something like this so I could be missing something.
@wingnut I'd recommend taking a look at your '99 manual and starting on page 8W-90-7. There are drawings of all the connector locations, harness routings, & ground locations. I'd go through the pictures & make sure everything is accounted for. I've done projects like this more than a few times (just not on a TJ) and I forgot to either hook something up or missed a ground lug every time. Hopefully some folks with first-hand experience will chime in soon.
If you want to post up some pics of the mystery connectors that can't find a home post up a pic of them, we'll help you find them. When you put everything back together their pigtail probably ended up pointing the wrong direction or something.