Sorry to resurrect, but I just joined the forums to cover a dual battery setup I'm working on, and I can't start threads yet...
I want to share because I have not seen it done this way yet and may help give some others ideas for mods custom to your needs. My setup uses an (almost) stock starter battery size (I believe stock would be BCI size grouping 24, whereas I am using BCI group 35), along with a group size 27 75 amp-hour deep cycle RV/marine battery as auxiliary. This is almost the same height and width as the 24 or 35, but about 2 inches longer.
To make this fit I had to make 3 adjustments (cannibalizing metal).
1) I cut out the bracket that the battery normally sits on top of. This gives more vertical room to play with, which was important for #2
2) I cut into the sheet metal wall toward the fender of the driver's side. Since I lowered the batteries in #1, I didn't have to cut much to allow the starter battery to slide under toward the fender. This gave me JUST ENOUGH room for the 2nd battery, except...
3) I did need to make a small change to the fan shroud. I didn't want to open a wide hole as many mods do, but I needed to remove the top bolt bracket because the 2nd battery rests snug up against the shroud and that tab would be in the way.
This is a WIP as I wait for my coolant overflow bottle to arrive so I can relocate that. You'll also see that I modified my fuse box, bringing it further toward the engine and away from the wall. I cut off the original mounting brackets from the fuse box and fabbed up a mount for it. This gives a bit more room against the driver's side wall to add a solenoid, secondary fuse box, or bus bars. I really like 42s' hinged secondary fuse bracket - I'll definitely be using that for inspiration.
Peace!