Hi Greg, the full diagrammatic electrical circuit for your Setec ST35 Series III is great for any of those who can follow the full circuit diagram. However, for those that cannot, I can tell you a fair bit about this unit as I have attempted to do something about the low charging voltage put out by this unit as I have the same unit in my Penguin only the 20 amp version. (ST20)
The main problem is that the voltage output to charge the battery is limited to only 14.0 or maybe 14.1. This may have been very suitable for GEL batteries which only require 14.2 or 14.3 volts for a FULL charge. However, this is not satisfactory for AGM batteries which really need 14.7 volts for a FULL charge. In an effort to alter this or get around it somehow, I have tried a few different ways including applying a 240 volt AC "smart" charger directly to the INPUT wires at the connector (pins 8 pos and pin 10 neg earth return) to charge a low battery. Whilst the input voltage from the charger reached 14.7 volts, the actual charge voltage at the battery did not get any higher than 14.0 volts (but no higher!) proving that the reverse bias resistance of the power diode in the input circuit was reducing the charging voltage by 0.7 volts. Looking at the circuit diagram (basic schematic), I decided to dismantle the unit to see if I could remove (or bypass) the power diode by following the output wire from the Setec. I found the diode eventually buried in the electrics!!. It is attached to the main chassis which acts as a great heat sink for the diode which blocks any voltage/current from the vehicle battery when discharging. So as that was not feasible or practical, I gave that idea away.
So as I am still with AGM systems, I use my 15A 7 stage "smart" charger direct to van battery whenever I need to keep my van battery fully charged and only use the Setec in the van for charging when at a caravan park. The van battery gets a FULL charge from my "smart" charger when I get home.
It will probably be easier and cheaper to bypass the Setec charging system and only use it as a power distribution system. A separate lithium charger suitable for 240 volt AC and 12 volt charging from vehicle (with DC to DC ability to meet the varying charging voltages of "smart" alternators) would also be required to charge lithium batteries correctly with their own algorithm for charging. Good luck and I hope this helps.
PS. You are not the only one who has attempted to change things. There are some other members on this forum that have also had a go and may wish to add more technical experience.