I noticed a lot of people are getting this problem with the 3500mah batts if I was on my comp id link other threads id try a diffrent rom to see if it helps I'm currently using sd 4.5 with speedy v7 config and get good life and phone is very snappy. I forgot if asked already but did you try starting from square one by wipeing and flashing again.
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Sent from my DROID3 using Tapatalk