The mountainous terrain between you and San Francisco makes signal propagation very difficult to predict with the accuracy you can expect when there are line of sight conditions. There may or may not be opportunities for signals of a given frequency to reflect off of natural or man made features.
If you are seeing signals that are predicted to arrive at levels of -100 dBm and lower, you are doing extremely well.
A co-channel warning means that two or more stations are transmitting on the same frequency and the levels from the two are close enough that you can expect them to interfere with each other.
Adjacent channel warnings are an indication that the small amount of 'off-channel' power from a station one channel above or below may cause problems with reception of the neighboring channel.
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Lastly, what can I do to get better reception of the weak channels that I sometime get & sometime can't?
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When blocked by 1000' and higher terrain, that's quite close:
1) Move.
2) Build and extremely tall tower.
3) Go to other extreme measures. Example,
http://forum.tvfool.com/showthread.php?t=1286