So, you have these four batts in series/parallel, correct?
What gauge and length of cables did you use to wire 1) batt to batt, 2) batt to shunt, and 3) mega watt to bank ?
Thanks.
For comparison, I had a 16" length of 4ga, with cheapo ends, from neg batt post to shunt. I changed it to 2" of 2ga with heavy duty ends. The V drop went from .03 to .01, just thru that one wire. I have since wired everything with 2ga and heavy duty ends.
When you take your battery readings; with the pos probe in the usual spot; move the neg probe around to various posts:
1) to the 2nd shunt post (from battery) to determine V loss thru neg charger-to-shunt wire, then
2) to the 1st shunt post (from battery) to determine V loss thru the shunt itself, (compared to #1 reading), and
3)to the neg batt post, to determine V loss thru the batt-to-shunt wire (compared to #2 reading).
As for the .03v difference between charger and batts, if that has remained steady for any real length of time, that is as good as you're going to get at this time.
And make sure you use the same meter for each reading, not the handheld for some, and the installed one for others, as there could be a discrepancy. For example, my power supply, motomaster hand held, and uni-t clamp meter all show different V readings on the same circuit, so i only "trust" the motomaster to establish "true" readings.