Any further tweaking of the FMF programmer from what you have now will only hurt your fuel mileage even more. It's not a big change, but you do lose a few miles per tank full the more you turn up the gas on the programmer. I'm at sea level too. And I have the exact same mods you have except for a more open airbox setup than just the flapper mod. I have an X with 13/40 gearing and run 100% street. Currently I have my FMF programmer set to: 3,5,2,8,2,4.5
The bike runs like a bat outta hell as far as I'm concerned. I've tried a lot of combinations with the programmer and I think I have settled on these numbers. On average I get about 95-100 miles before the low fuel light comes on. In stock form I was getting to about 110-115 miles before the light came on. I'm not concerned with the lower mileage. It still beats the hell out of what my truck burns. I commute 35 miles a day with this bike, and it saves me a small fortune over a month's time. One of the reasons I bought it.
When you removed the charcoal canister, what did you do with the vent hose to the fuel tank? You should keep it up high above the fill cap or you may notice a little spillage when the tank is full. Other option is to cap that fitting off on the tank and buy a vented fill cap from the 49 state bikes. We don't have the canister, so the tank is vented through the cap on our bikes. Your California cap is non-vented.