I can't answer your questions but will add...
I think the wire fron the isolator back is 4awg on my 2000 Excel TD. Somewhere in the rear it changes as I'm pretty certain both sides of the red master switch are 2/0, with 2/0 to the battery. I may be mistaken these might be 2awg but bigger than 4awg. Where it changes I have no idea but one side goes to the battery and it is protected by an 80amp breaker that is labeled "80 amp charge line" with this big wire on each side. There is also a breaker there labeled "30 amp power conveter" these are I believe 8 or 10awg. ( I'm used to working with residential off-grid solar where we use primarily 2/0, 4/0 and 10awg, sometimes 6 or 8awg but not often.)
I do like your idea of a busbar to connect the existing wires back to... alternator output, Chassis Battery and a line to the DC to DC charger. It would make clean in place of the Isolator.
I have wanted to do what you describe but I'm unclear exactly which wire is coming from the isolator and if it makes other stops along the way. I found it impossible to trace it under the van.
We wait for those who know more!
Your wire sizes are starting to make more sense now.
You think you have #4 to the coach from the isolator with 80 amp breakers in that cable. That is how many of the vans of that era were done, including our 07 roadtrek with two 12v wet cells.
You think you may may have a #2 cable for the battery or batteries to the disconnect. This is also very typical of the era and many, like ours had #2 battery cable to a binding post and then to the inverter charger as a smaller wire for only and 45 amp charger, 700 watt inverter, but no disconnect. My guess is that is all original and fused properly.
For the isolator all you need to do is disconnect the starting battery and leave the coach battery connected. The only wire you should see voltage on would be the one to the coach, so you will know which it is. Then disconnect the coach battery and connect the starting battery and you should see power on one cable, so you know which one that is. The other large wire would likely go to the alternator and be easy to trace if there is one. You would need the wiring diagram for the isolator that is probably online but probably the alternator and battery cables would connect together like they did stock. If there is a separate alternator cable that would also connect. Put them all on a busbar. Amazon has a lot of them, some better than others, look for thick bars and at least 8mm/5/16" diameter studs.
In general, all you need is to have the alternator and starting battery plus the cable to coach all together and should need nothing else like run sensing or such that might be on the isolator.
The wire to coach would go to the B to B charger and then to the coach batteries, or it would go to the new inverter with it's 110v output to a new transfer switch and then to shore charger. Both systems are quite simple, but B to B is probably a bit easier with only one addition and no 110v to deal with.
Sketch up both wiring diagrams and it probably will get pretty easy to see how they will work.