to starter is Standard practice. Why run a large cable from alternator
to switch (2awg +). When you already have a large cable running to switch near by that isn't being used with engine
you need to measure all the points with the engine
running. Voltage at alt post, voltage at both sides of shunt, voltage at starter post, voltage at battery
switch, voltage at both batteries. follow the power and sense wire for the reg (if If has a sesnse some just use the power wire). Compare it to vaule on reg screen
Use the same ground for all measurements. Ie start battery
ground. Then retake all measurements with the alt ground post, or engine block.
Then you can isolate if problem is in pos or neg cable sections
If should be easy to find the section loosing voktage. Abd fibd the problem. if you are losing voltage slowly at each point the. You'll have to re do everything with bigger / better wire
Do the test with bAtteries drained some. If they are full and alt isn't putting out any current
you won't see any drops or problems.
If you left the factory orange cabling (probably a 10 awg?). This is Likly a main factor. a 100a alternator
connected to starter post should be a 4awg or 2 awg. And bigger if run to batteries instead. Ground wire if there is one should be sane size to engine neg.