could you disable terrasync and only use the old ksfo scenery to check that this is due to old vs. new scenery ?
you said that your framerate was previously ok in 2.12 - what was it (fps/ms) ?
Also, have you tried the instructions at:
http://wiki.flightgear.org/Howto:Debugging_extreme_lag ?
These should help you determine your best frame rate (while disabling everything else), so that you can find settings that are having a massive impact, and keep those disabled.