My 01 will be needing batteries one of these days also, and I've done a lot of reading on here about the 31's. A slight mod to the drivers side battery tray is required for the 31's - something like using a dremel to cut away a plastic gusset. A lot of folks run 31's and a few have said they required no mod to the trays at all. The vast majority however had to cut the tray a little. You will need to make or modify the hold down bracket/bolts for the 31. There are no clearance issues with the hood from what I've read.
I don't know much about the size 65.
In Optima brand, a couple of differences between the 31 and 27 follow:
D27F D31A&T
830cca 900cca
140 155 reserve capacity
53. 2 59. 8 weight
In a dual battery setup, are we really gaining a lot by going to the 31's over the 27's?