If you hold a US passport there should be no problem to pass immigration and make your way to the FCT. Luggage will be checked through, no worries about this. Finally passport control and screening in the FCT is a breeze.

For the FCLs, the one in the Schengen area (close to A65/A25) is the best one. Both non-Schengen FCLs provide a limited offer only.

You are correct, til end of 2008 Switzerland is a No-Schengen country. So you do a transit (Non-Schengen to Non-Schengen) connection. However, AFAIK immigration is easy going for all US citizens in FRA.