I don't know about 2007, but the LLY's have a problem with unsealed (on the top) batteries on the passenger side. Look to see if water from the cowl runs down onto the top of the passenger side battery. Water then seeps through the caps on top.
The solutions are to either (1) use batteries that don't have vents/caps on top, or (2) cover the top of the passenger side battery. I bought a battery case at Walmart, cut the top a little to clear the side terminals, plugged the vents it had, and strapped it on, discarded the rest of the battery box).
It turns out the gassers had an extra brace (I think you can see mounting holes) if they had the 2nd battery. The brace would direct water away. Diesels don't have that piece.
2004.5 Silverado 3500 SRW 4x4, D/A (LLY), Ext. Cab, Long Bed
engineer837 aux rad, TxC CAI, LBZ MP, Scangauge II, Nicktane aux filter head, KD lift pump, 2008 PS pump, 2011 hydroboost, Frederico Swaybars, Rancho 9000XL, Torklift StableLoads, BFG AT/KO2, Lance 835 Camper often in the bed.