I think you may be missing a point here. The fish poop that creates the high numbers of Ammonia eventually gets consumed by the bacteria and they grow on all surfaces. That's gravel, rocks, pebbles, plastic plants, filter parts, all surfaces. You should not be removing or cleaning any of these until you are well thru the full cycle and even then the tank needs to "mature". I personally would not gravel vac AT ALL until my tank is well established or if you do, do so sparingly.
Have you tested your source water to see what is in it? I have .25ppm in my tap water so I use Prime as it neutralizes everything. The ammonia lock is probably what is keeping your fish safe but it still gives you positive numbers I believe since it is still present. Does that make sense?
When the store tested the Ammonia was it dark green??