Your system has 3 parallel pairs of batteries arranged in series to give, effectively, three 24V batteries in parallel. Try to keep all the cables from each of the 3 negative poles the same length so they have same resistance. Do the same at the positive side of each 24V pair. The “Wiring Unlimited” reference linked above gives good guidance in section 3. All 6 batteries should see identical cable volt drops both under charging and when under load. For the longevity of your new batteries, it may be wise to invest in battery balancers too, considering the asymmetry of the physical layout you are proposing.
For the shunt connection I would route the 3 negative poles to a common busbar and connect the busbar to the battery side of the shunt. I’d connect the load end of the shunt to the earth and all the negative cables returning from the loads. The Shunt manual does not recommend stacking more than two terminals on a post so use another another busbar for this if necessary.