and blew the starter battery fuse I installed
Is this one of the 80A fuses installed between the batteries and ACR? If so, then you have something regarding the new switch and ACR that is majorly wired incorrect.
The alternator will not have any effect on the engine starting or not. Only charging or not charging once engine is running. So, if you are unsure of how the new alternator needs to be wired, put the old back in as it was originally for now.
To diagnose this, you will need a digital volt/ohm meter, and know how to use it. Once the cranking issue is resolved, you are going to need an accurate schematic for building the dual bank system.
Michael
Mikes Liquid Audio