the ss guys are using the SSR battery box which mounts where the spare tire goes, so the shortest run is down the frame rail to the starter. you could probably use 4ga welding cable without issue. then you take the other end of the existing starter cable, that terminates at the battery terminal, chop that and put a lug terminal on it, and bolt it to the fuse box. then take the alternator cable at the battery terminal, chop that, throw a lug on it, and connect that to the terminal as well
if you are going to mount the battery inside, it may just be easier/shorter run to just run your battery cable straight to the fuse box and connect your starter and alt there as well. depends where you put it. the rear passenger quarter panel, where the compressor goes, is a nice hiding spot if you can get a little battery shelf fabricated
for the ground, ground your battery to the frame and make sure you have decent frame->body and frame->engine grounds up front. just trace the wires from the original battery terminal
forget about the rear fuse box. there is no reason to mess with that unless you feel like spending time and money for no reason
it up 
hmmm... i would have the battery behind the passenger (in a case and bolted down VERY good)
I would make one run to the rear block with a 125A fuse, and then a second run up to the front as originally planned. Then disconnect the megafuse and power connections that run to the rear block. That should probably do the trick. 
