Oh and also, on overnight charging, the phone just stays at 50% (I'm guessing that the heat is using the rest)
Tap, Swype, and Talk.
Yeah, I would go ahead and go back to stock and see if that changes anything.
Sent from my RZRecovery'd Overclocked, and ROM'd Droid.
Well, I am late to this party, but I have also noticed that when the phone gets too hot the battery stops charging. That's why an extra battery and a battery only charger was invented. Silly people, that jack on the phone isn't _really_ meant to charge it, it's only for hacking and USB transfers and such, lol.
Other than that I don't have any good advice to fix you up. The only time I use the jack for charging is in the situation that guidot posted, in the car using nav in the car dock. When it starts to get too hot, I start turning on the defrost on as cold as I can get it, FWIW.