AC's Trans Am route south on 93, etc., to Hamilton, Darby, Sula, Wisdom, Jackson, Dillon and Twin Bridges is quite nice in most places. As noted, from the Jct. of U.S. 12 and U.S. 93, there is a spur into Missoula. You then back track south on U.S. 93 to continue on the Trans Am.
This summer we did a loop from/to Missoula. We followed the TA for a few days and then did our own thing to get back to Missoula. We did pass through Twin Bridges but did not stay on the TA to get there. Instead, we took the Pioneer Mountains Scenic Byway off the TA (after descending Lost Trail Pass) to Wise River and then headed through Divide and Melrose and took the Melrose Bench Road, which is not paved, to Twin Bridges. The advantage of this route is that you get to do the scenic ride to Lost Trail and Chief Joseph Passes into Wisdom then Lost Trail Pass after Jackson. The Pioneer Mountains Scenic Byway and state route 43 to Divide is a fabulous ride. Melrose Bench is somewhat of a challenge due to the surface and some climbing, but worth it. Overall, prettier than staying on the TA to Dillon IMO. Lot's of camping on the Byway (U.S.F.S. campgrounds and dispersed camping) and in Divide (BLM along the river for $6 and Melrose (private).
Send me a private message if you would like some route options through this neck of the woods. Our route back to Missoula from Twin Bridges included Rock Creek Rd. Off the beaten path and very scenic. Most of it is not paved, but we had no problems on 37c tires. Going in your direction, you'd go through Phillipsburg, Anaconda and Butte then over Pipestone Pass (state route 2) and then come down state route 41 through Silver Star into Twin Bridges to hook back up with the TA toward Virginia City and Ennis.
Every day but the last is chronicled here:http://www.crazyguyonabike.com/doc/?o=1&doc_id=4964&v=Ao
If you stay in Twin Bridges, check out the free Bike Camp. Great place with a shower, etc.
Agree that Missoula and the AC headquarters are nice places to visit. Some relatively cheap motels in town and a nice KOA an easy ride from the center of town and right near an REI if you need supplies.