Using an MCP73831 charge controller with a BAS3007A Low VF Schottky Diode Array
I was able to solve this by using an H-Bridge wired as an active rectifier. By using the recommendation here as inspiration, I bought a MOSFET Array 2 N and 2 P-Channel H-Bridge (DMHC3025) and wired it up as shown in the image below. This removed the voltage drop across the diode bridge and fix the inconsistent performance of my charging circuit.