Lorin:
Here's what I see so far -
Alameda County looks goofy. You have 13 channels in there. It looks like all the control channels are there, but I would edit it so you have _only_ the control channels:
866.9375, 867.4000, 868.0875, 868.7625
From the South Bay you should only be able to hear 1 control channel at a time.
Santa Clara - all the freqs are there, just not in order. Since it's Mot I don't think it should matter, but it doesn't hurt to put them in order. I only have the 4 control channels in my radios, and they work fine, but I've never checked to see if they use more than 4 channels in rotation as control.
Note: Santa Clara is patchy, even in the city itself. Try a different antenna, or location.
Livermore - You have extra channels that are not a part of the system. Livermore should be:
856.9625, 857.9625, 858.9625, 859.9625, 860.9625
Oakland is also messed up. You need to put Site 1 (APL) and Site 2 (Seneca) in separate TSYS objects. They're like separate systems. It's also EDACS, so look carefully at the LCN order for Site 1. There are several blank LCNs that are hard to see.
Oakland P25 should be: LCN1: 866.1250 LCN2: 867.3000 LCN3: 868.1750 P25 AUTO
San Francisco: You have control channels from both subsystems in one object. I would separate these and treat them as separate systems. They have the same SysID, but I never see any crossover of talkgroups. Maybe it's different within the actual system coverage area.
Let me know if any of this helps.