I had aspirations to put a center mounted rod locker in my Tracker like the new bass boats have. I hate side boxes. Unfortunately I never got around to it.
In my situation I was going to build an enclosure that extended from the middle of the front deck with a flip up lid, and insert several thin wall PVC tubes into the vertical wall of the front deck inside of it, that would go pretty much all the way up into the bow area. Rods would slide up into the tubes, and you could get whichever one you wanted without taking the others out.
You can remove some foam but you will need to add an equal amount back somewhere, as close to where it was as you can.