With the box checked and the blanket waiver code assigned to the COVID vaccine part of your DS-3025, that means your vaccinations are considered complete for the purposes of your AOS. The C3 code indicates the vaccine is contraindicated by the physician due to allergic reaction. Very rarely do USCIS Adjudication Officers overrule a physician on a medical decision. They will on procedural issues or incomplete paperwork but rarely on strictly medical judgement calls like vaccine contraindications. Just send a copy of your DS-3025 as supporting evidence along with your I-485 when you file.
As far as filing the AOS within the 90 days, there is nothing that says you have to - HOWEVER if you do not file within the 90 days, once you hit day 91, you are out of status. It's all about your risk tolerance, especially in light of the incoming administration's promise to crack down on those in the country unlawfully. If you file the I-485 and have the receipt number, you are then in a period of "Authorized Stay" until it is adjudicated. I would highly recommend filing before your 90 days has passed.