To answer your last question first. the fuses should be closest to the batteries.
In a parallel bank only one fuse is required, on the positive feed wire to loads.
On the wire going from the positive bus of the house bank to the Perko switch the fuse should be larger - ANL preferred. Alternator output fuse should be an ANL as well. Or MRBF fuses on the bus for each.
The rest looks pretty good.
In 98% of situations yes but there are a number of boats out there where half the bank is on port and half on starboard. In order to "protect the wire" it is best in a situation like that to fuse both halves of the parallel bank.
Jos does not need that on his boat as the location will only fit two group 31's and is too short height wise for 6V batts, unless you were to really modify it. So he really only needs one fuse on the house bank.
In marine electrical terms a "source" would be considered AC shore power, inverter, generator or batteries. An Iota type charger, than can act as a power supply when the batts are removed could also be considered a "source" when acting as one.
Anything connected directly to the batteries should ideally get a fuse as close as possible. ABYC calls for 7" but that is darn near impossible on many boats and on your MRBF's may or may not fit under the lid depending upon brand of battery. I know they fit with Deka's because I recently finished 34 MK I with Deka's in it, but it is darn close to the lid. Most battery chargers are either internally fused or have fuses close to the charger so there should also be a fuse at the batteries.
The only small item I might change is to put the battery monitor sense wire on the positive post of the house bank for the most accuracy. Your shunt will go between the DC negative buss and the battery.