The schematic shows a 'zero ohm' shunt coil in series with the negative DC output lead ... It appears to be a heavy gauge piece of copper in one of the photos. Just guessing, but the purpose of that coil is to act as a high frequency impedance and smooth out the DC waveform as it goes to the batteries.

Cool thank you for informing me of that, I will plan on keeping that in like with the DC negative (Black)

 

If possible I do not want to use the any of the control circuitry, just the transformer and SCRs, unless something else is needed from the original diagram

It is not possible to just use the SCRs as they need the control circuit to trigger them at the appropriate part of the AC cycle to control the output voltage.
A new control circuit could be made.

 

It will be easier and cheaper to get a 500AH 12V deep cycle battery and a 20A battery charger.
Forget the 48V.

 

The problem is your transformer output voltage it too high for your application. The 48V to 12V converter will go bang I expect.
Without rewinding the transformer, I do not see an easy way for you to use this charger safely. And I doubt the control of the charger is able to be set to work as a 48V supply without voltage overshoots high enough to cause damage to your regulator. Someone else may have more ideas.

I am now considering rewinding the transformer, would only the secondary windings need to be changed? More windings? Less?

I believe I will have to test the secondary outputs as I do this.

 

Assuming I can get a transformer to produce either 48vac or 12vac I still have the problem of converting it to DC. A full bridge rectifier has been mentioned but my existing SCRs will not work without some sort of control.

would it be easier to use the existing SCRs and purchase some sort of control circuit for it?

or to order parts (Diodes in order to wire a full bridge rectifier circuit that could convert it to DC without our the need of a control circuit?

 

You will have to use some sort of control for the SCRs.
They do not work by them selves. So, trying to make use of the original sounds like the best way for a start at least.
But, really, the charger is not suitable for your use without pretty extensive mods.
And, high current bridge rectifiers are not real expensive.

 

In order to alter the triggering phase of the Thyristors, you need to understand the circuit board, it's probably set by the chip or maybe able to alter the firing angle,, need better pics of the pcb and chips..