So, like a madman I've given it my all today to see what I could do. I replaced all the old cable ends (they were outside from an old satellite installation and the ends were pretty corroded).
I went back and forth from the root adjusting the antenna, using the amp, not using the amp, messing with the ground, in the middle of the day it seemed to start getting significantly worse and I couldn't get it back. Felt exactly like this: http://xkcd.com/349/
After much, much trial and error I think I got the ideal direction for the antenna. To the south east of where I live there is a big mountain, if I aim the antenna way west around the mountain, I get NBC pretty good but lost ION. If I aimed it way east around the mountain I got ION ok (not great), but couldn't get NBC. The best location is pretty much pointing directly at the mountain between a gap in some trees.
Weirdly, my second TV actually seems to be handling the NBC signal better than the first. I've been testing this by having them both on and my main tv (55" plasma) seems to cut out a lot more than the second tv (26" LCD). There were times where the primary tv would cut out for a few seconds where the second tv wouldn't have any problems.
I'm still not convinced the amp is doing anything. After getting what I felt like was the ideal position of the antenna I started messing around using or not using the amp. With the amp installed the signal strength doesn't change and the picture stability (not sure if that's the right word) doesn't appear to change.
I also tried installing a grounding block with a 10AWG solid copper core wire for a ground wire but that reduced the signal strength by 8% or so. Would hooking up a ground directly to the antenna cause any signal issues?
Getting a good workout today though, I've probably gone up and down off the roof more than 30 times.
Thoughts? I know the amp at the antenna is the better choice but I might try a distribution amp just so I can be sure I've exhausted my current options (besides getting an even bigger antenna or a rotator).