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PatSiesta said..OK here are a couple of photos of the mess! I'm sure there have been worse...

Yep, that looks pretty normal for a boat.

If you take the time to chase the wires, buy yourself a little cable labeller like a Brother P touch, it'll pay for itself in no time just for your sanity!
At the end of the day, you have two networks you want to try to connect, sinks and sources.
Sinks are all your field, or 'edge' equipment like wind sensors, lights, radios, fridges etc.
Sources are all your head end equipment, like batteries and your PC or chartplotter and charging systems.
When drawing it out, I always start with listing my sources on the left hand side and my sinks on the right hand side of the paper. I then draw a line from each source to the related sinks I want it to power/communicate to. Do this for every source. Then take all that horrible scrawled mess you've just created and enter it all into a spreadsheet. The cabling will start to sort itself out into some form of order and logic.
A device can be a source and a sink. For example, batteries gets listed in both the source and the sink columns. It is a source for field equipment, but they are also a sink in relation to your charging systems (which is another source). So it gets an entry in both columns.
This approach can also help sorting out your protection systems. Head end devices get circuit breakers and isolation switches. Field devices get fuses and no isolation.
There will be some edge equipment that is high current, like windlasses and electric winches. These are still edge devices in the spreadsheet but might get some special treatment like increased cable gauge and circuit breakers rather than a fuse.
If you think of it like sources and sinks, how to re-terminate and patch cabling gets a lot simpler. This is where your bus bars comes in, what termination and where to use it will usually become apparent after thrashing out which source/s is needed for which sink.
With the charging sources, don't just connect them to the battery banks. For example, rigging shore power to not only connect to batteries but also to the fuse/distribution panel for powering systems can be super handy.
Best of luck with it!