Non continuous OBD monitors won't set

I've been trying to inspect my car for months in NY. I have read just about everything on google about e46 OBD readiness monitors and drive cycles and have tried it all. The 5 non continuous monitors will not change from "Not ready".
Here's the back story on what I have changed:
Tried for inspection first time(bought car a little over a year ago). We discover that my SES light doesn't illuminate, inspection shop turns a blind eye. Upon plugging car in, I have catalyst and evap as not ready(drove 10k miles prior). Automatic fail. I also have codes for evap very small leak and low fuel misfire.
I replace my fuel filter, gas cap, and find the vacuum line from filter to intake broke. Clear codes with Torque app. Drive a bit, secondary air system bank 1&2 codes come up.
I check secondary air system and find the vacuum line broke in two. Repair that, clear codes again.

Now I have no codes and all 5 non continuous monitors still read not ready. I have driven over 300 miles and specifically have spent over 100 of those doing drive cycles. I'm at a loss as to what to do next and hope someone has encountered this before??