William Sullivan's "green book" mentions a long loop that involves some bushwhacking, and I found basically the same loop described in a Sisters newspaper article. Both sources said that you should do it clockwise, but I'm stubborn, and I have a GPS (two of them if you count my phone), and I don't like back-lit mountains in my photos, so I decided to do it in reverse so that I was starting on the east side in the morning. (Click here for an interactive Google Map)
So I woke up at oh-dark-thirty and got on the road by 5:45am. I stopped in Salem to pick up lunch (FYI, the deli section at Winco has excellent croissant sandwiches for $2.48), and got to the Santiam Pass trailhead for the Pacific Crest Trail at about 8:30. This is right in the middle of the burned area from the huge 2003 B&B Complex fire, so the first 4 or 5 miles (as well as the last 4) looked pretty much like this: I headed east to Square Lake, then north to Booth Lake. In places, the trail was almost invisible because of the out-of-control snowbrush shrubs (Ceanothus velutinus) growing on either side. Both lakes were pretty unremarkable, but I finally started getting some views of TFJ near Booth Lake. Scarlet gilia was EVERYWHERE in the burned area; at first I thought all the red must be paintbrush, but nope. Of course there were lupines and beargrass all over the place too, but the beargrass is pretty much done. Thistles and cat's-ear lilies were common, as well as a couple kinds of penstemon. And butterflies.... holy crap, I've never seen so many butterflies in one day. And of course the usual assortment of bumblebees, flies, and beetles: When I got to the bottom of a little draw east of Martin Lake, I headed off-trail and uphill to the west (first blue section on my map). There was no water flowing anymore, but you could tell where it had been a little wetter, based on the vegetation. I had to step over a lot of fallen burned trees, but it was easy going. Martin Lake was very picturesque, partly because it was half-surrounded by — get this — UN-burned trees! It would have been a great place for skinny-dipping, except I didn't want to give the mosquitoes any more of a target. I considered bushwhacking up the ridge on the north side of Martin Lake and trying to reach Summit Lake, but I was afraid it might be hairier than it looked on the map, so I just took the "easy" route (first purple segment) and found my way up to the PCT. It would've been a piece of cake if I'd bothered taking my trekking poles off my pack.
From the ridge, there were awesome views to the east and south. This photo is actually from when I came back this way in the afternoon (better light): I went north on the PCT for about a half a mile, and finally ran into a couple of patches of snow. I was looking to see if there was a good place I could leave the trail and go up the ridge that forms the south side of TFJ. At a switchback, I found a good spot, and battled my way uphill through this sort of stuff: But most of it wasn't quite that rough, and this time I did get my poles out. Check out the view to the south from that ridge; the two lakes in the foreground are Booth Lake and Square Lake, which I'd passed earlier. Oh, and the view of Three-Fingered Jack from up there wasn't bad either.

The rest of the hike was uneventful: a five-mile descent through a bit of healthy alpine forest and then a whole lot of 10-year-old fire damage. I was glad I'd brought my iPod. I did find some water lilies in a cute little pond near the end, though. (I'd post a photo, but apparently I've reached my forum attachment limit!)
Overall, it was about 13.6 miles (not counting wanderings to chase butterflies or interesting wildflowers), with between 2000 and 2500 feet of elevation gain. There were quite a few mosquitoes — both near the lakes and on the PCT where the snow was melting — but they had a healthy respect for DEET.
Here's a 3-D Google Earth view of the interesting parts: And more photos: http://adamschneider.net/photos/2013-07-tfj/