In Arizona, the http://verdecanyonrr.com/ runs a pair of F's, in California, http://www.fwry-blog.com/ may be running F's, and the http://www.csrmf.org/ usually has a Santa Fe F7A and F3B on display
http://www.mtrainierrailroad.com/ They have a former NP F unit, in NP paint, somewhat faded. http://www.oregoncoastscenic.org/ They have a former GN F unit, in somewhat fading GN paint.
I might suggest checking both of these sites. http://www.thedieselshop.us/SurvivorsEmdFs.HTML https://sites.google.com/site/railwaypreservationphotoindex/by-railroad
B&O Railroad Museum, Baltimore, MD. WM #236 F7. Don't know whether this unit is in running condition or not. http://www.borail.org/236.aspx Dom
Rio Grande F9A #5771 and F9B #5762 at the Colorado Railroad Museum in Golden. Cosmetic restoration only, non operating.
The Illinois Railway Museum has a CNW F7. I believe it was given to them by Metra when the E and F units were retired. The museum runs it with matching Bi-level cars.
The Feather River Railway museum in Portola California has a F unit or two in operating condition from the late Western Pacific.
Contacted the Feather River Railway Museum. As of now the WP 917-D is operable and is ran at times Just FYI
The Galveston Railroad Museum in Texas has two operating F units painted in the Santa Fe warbonnet scheme, although the're actually former SP units. Does E units count? The Orange Empire RR Museum in Perris, CA has a restored and operating Union Pacific E passenger unit.
Niles Canyon RR museum has Western Pacific F7 918D. California State RR museum has Western Pacific F7 913. Western Pacific RR museum has Western Pacific FP7 825A, F7 917D and 921D.
Not a museum, but the Columbia Star Dinner Train has a pair of F units. Their heritage includes Seattle & North Coast RR, Burlington Northern RR and the Great Northern RY. http://columbiadinnertrain.com/
Exporail, the Canadian Railway Museum, has an FP9A, VIA 6309, ex-VIA 6528, originally CNR 6528. Not known if it's a runner or not, but here she is: IMGP2485_VIA-6309 by Mike VE2TRV posted Jul 2, 2016 at 9:46 PM It needs a bit of work, and I hope they repaint it in the original 1950s CN passenger scheme.
I looked up the Columbia Star Dinner Train on Google, and it says it closed due to debt to the city it operates in. That's too bad, it seemed to be enjoyed.
Interesting! Looks like there are more preserved WP F units than for any other railroad. Any B units?
Some more possibilities: The Museum of Transportation in St Louis lists GM103, and FT-A demonstrator and SOU60603, an FT-B The Kentucky Rail Museum shows ATSF2546, a CF-7 Royal Gorge Route in Colorado uses F7's
Conway Scenic Railroad, North Conway, NH. These F7As are original B&M locomotives, now actively hauling foamers and tourists through Crawford Notch.