I did make a mistake, though.
The shift rod is the same diameter all the way across. Don't know why I thought it was stepped.

Basically just measure the rod from the groove to the 'washer', then measure the thickness of the shift lever and subtract that from the lengthe of the rod, cut a piece of tubing that length, and slide it onto the rod.
Use some electrical tape to build up what's left to the diameter of the hole in the shift lever, then cut it off just behind the groove.
Slide it into the hole on the shift lever, and put an E-clip of the right size into the groove of the shift rod.
You want to build up the end of the rod so it doesn't flop around in the hole of the shift lever. The tubing is so you can get a nice snug fit between the E-clip and the face of the shift lever.