I'd love some lighting tips from those who have built, or live in, timberframes. I am adding a 12x34 one-story, three-bay, flat-roof addition onto the south side of my 30x34 two-story timberframe. Both house and addition have 8.5 ft ceilings.

We underlit our original house, and I would like to avoid that for the addition, but don't have much insight on how to do this right other than to run an excess of wires and track and work it out after the fact.

I'm thinking of centered ceiling fan/light combos in each bay, plus paired runs of track lights along the joists within each bay.

Any good rules of thumb, success stories, things to avoid, or other tips? All thoughts appreciated.

Lots of options. Some common solutions;
Router a channel on top of rafters and such to contain your wiring before you put the top on.
If you are using sips for roof they can contain wiring in channels or imbedded pvc pipe.
Where you exit timber tops to the fixtures there are wood look alike plastic channels for containing the wiring to the ceiling fixture(s).
(so you dont have to fabricate boxes)
In any case you are looking at some very careful prior planning so the wiring just kinda falls into place.
You may want to consider X10 so you have wireless dimmer control and such from a hand held remote and/or a central control location.