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The battery shouldn't hit the hood, but double check incase you have one of those thick battery matts. If its just the hood out of alignment then loosen the hinges at the firewall and adjust accordingly
I'll check that out when I get back to the truck later this week
I would suggest some insulation pads on the battery terminals if they are hitting the hood.
So are you saying they are too tall ?? DarkOverCast said they fit just fine ?
OR is the problem the OEM Hood insulation ?
EDIT: you could adjust the hood up just a bit so it is even, that won't hurt anything.
Are the batteries sitting all the way down flat in the trays ?
They seemed to be sitting flat it could be the insolation in the hood it has some left but it's missing a lot good thing is my terminals do have rubber covers