Well, I spent some more time fiddling with the antennas. I've actually turned the VHF beam southeast to try and pick up KSBW and KCBA (Salinas) from Fremont Peak. Here's where things stand:
DTV stations that come in perfectly, with no issues: KPIX, KQED, KBCW, KICU, KCSM, KTEH, KKPX, KCNS, KSTS, KTSF, KGO, KMTP, KBWB, KFSF, KNTV
DTV stations that are marginal - most of the time they're fine, but sometimes they pixelate or drop out: KRON, KTVU, KDTV.
DTV stations that come in at least sometimes, but are not 100% coverage: KSBW, KCBA, KRCB.
DTV stations that don't come in at all, but I don't see why not: KTLN, KTNC.
If I go up to the roof and aim the UHF a little bit more northerly from where it is now, KRCB, KTLN and KTNC seems to come in a little better, but KTVU and KRON start getting more marginal. We're talking about maybe 5 degrees, with an antenna whose half power beam-width is more like 30 degrees.
The only thing I can think of is that perhaps the pre-amp is being overloaded and that it's pushing the weaker signals down a little. If that's the case, then the analog shutdown next February will help somewhat.
The shutdown will certainly help KSBW and KCBA, which currently suffer co-channel interference from KXTV-TV and KOVR-TV. We also will likely be able to pick up KAXT-LD. At the moment, KAXT-LD is co-channel with KTNC-TV. One worry is that KRCB-DT is going to be co-channel with KMUV-LP, but fortunately it will be in the opposite direction, so the antenna's front-to-back ratio should bury it. The bad part about that is that we will have no chance at all of picking up the other UHF channels from Fremont Peak: KQET and KSMS. But KQET is redundant if you can receive KQED and KTEH already (KQET-1 is the same as KQED-1, KQET-2 is the same as KTEH-1 and KQET-3 is V-Me, which is on KTEH-5), and KSMS is a Univision affiliate like KDTV.