Well, I wasn't able to track down my notes - I might have tossed them after finishing the job, since they weren't all that complex. Now that it's the weekend and I'm not behind that company firewall, I can elaborate a little on the wiring conversion:
The older-style mirrors use the same 3-pin plug as the dome lights (it's also used for some sensor in 2004-2005 Ford Super Duty trucks, but exactly what escapes me. Scavenging the connectors from XJ dome light harnesses or broken mirrors is probably easiest). They use a "2-axis" system - one motor for up/down, one for in/out. Direction is handled by which polarity the 12V and Ground are connected to the motor through the control switch; the two "ground" lines from the motors share one pin on the connector (usually the black wire).
On the newer model mirrors, Jeep went to a larger, six-pin connector that has two rows of three pins. Some later mirrors are heated - when looking into the connector with the locking "nub" on the top, the two wires for the heating element should be the right-most pin in each row. The mechanism inside the mirror is basically the same (an up/down motor and an in/out motor), the other four pins are for the motors (same two-axis system as the old mirrors, but the two "grounds" from the motors get separate pins now.
I'm not sure if all 97-01 power mirrors use the same colors on the wires, and I didn't have a schematic, so I simply applied 12V and ground to the pins in pairs until I figured out what pin combinations caused the mirror to move in each direction and wrote it all down.
Then, I pulled the door apart and removed the old mirror. I twisted the wires onto the "new" connector and experimented until the mirror movement matched the direction I pressed on the switch, then I replaced the temp twistings with heat-shrink crimp splices and started reassembly.
Once I had it together I found that (as noted in several writeups on the topic) that there may be interference between the newer mirrors and the window trim; rather than try to trim the trim, I elected to just torque things down and fill the gap with a bead of black permatex RTV to seal the mirror to the door. Seems to be working fine, and isn't noticeable unless you go in close specifically for it.
Finally, I sprayed some white lithium grease into the pivot points (you can spray in from the bottom through a little cover you can pull, and from the top by folding the mirror half-way in) and worked the mirrors back and forth a few times to loosen them up, as mine were a bit stiff from sitting a while.
Best of luck in your swap - all in all, it's probably an hour or two of work for both sides, if you're fairly efficient with getting the door panels on and off.