Ok, so updating this for anyone who finds this in the future. The problem was my OBD2-to-Honda 20-pin cable. The pin-out was incorrect. I re-soldered it and hopped in the car. without a charger on the battery.
When I changed the map in my car, I was prompted to enter the IPAS code for the DME twice(once for old and once for new). I was never prompted to confirm my vin. The loading screen took approximately two minutes(the PST2 clone is on a laptop with an SSD). After, I was prompted to turn the car off(engine was not running, key just in on position) and turn it back on. I "confirmed" the car was programmed correctly by starting it without stepping on the clutch. Drove the car 1/4 mile and have now parked it for the night.
