I was told the 'Sonoma's has a pitted-out boiler and some other significant 'issues'; but I don't know if this is true or not. If I recall the last steaming of 'Sonoma' was by the P.C.C. of R&LHS at the 1939/40 Expo at Treasure Island in the middle of San Francisco Bay on a short bit of demonstration track. I believe their other acquisition from the Nevada Central (the Mogul, ex-Nevada Short Line) was also used there. I believe the PCC's locomotives (or at least some) were stored in the Oakland Roundhouse for several years until
Like the SCR "Jupiter", the "Sonoma" would now be the sole survivor from the NPC. The cab forward would've made an interesting piece in the CSRM if it fared the years until today...despite its easily arguable hideous appearance. I sort of liked the thing.
As for the Smithsonian and the Jupiter; I wouldn't think the 'preservation of historical fabric' movement would be as much of an issue as politics and bureaucrats if someone tried to get it out of there. As Phil said, the locomotive was reboilered for the several decades serving 'south of the border'; at best, it's 1876 America from the saddle down. I don't know any details, though. When I last saw the locomotive, it was still part of the bicentennial exhibit opened in 1976 at the Arts and Industries Building of SI.