My word of advice if you plan to work with EE's is to first think about component annotations, follow rules for creating schematics and use engineering notations (prefixes) instead of scientific (1E-9) for component values. Your question is now pretty much split into two, 1. MPPT algorithm development and 2. Troubleshooting your main circuit. I would propose you move out 2. into SPICE, for example LTspice or PSpice and troubleshoot it there or just ignore the main circuit from your problem...

...and change it into an ideal magic block which takes input voltage, duty cycle request and outputs voltage accordingly and then focus on your MPPT algorithm.