I had this problem a few months ago and stopped baking to resolve it. I only baked enough to complete goals and I bought 3 ovens of each so I was done with main goals 3-5 days early. I then put the appliances in storage and didn't bake anything for a few days. I didn't do all the side goals because I only ever did them if I liked the prize decoration anyway. It took a few months but my counters are down to a reasonable level and I am at the point where I put out the counters I want and am getting back to the layout I want. I am also only down to 2 counters with over 100K food. A few with over 30K food and the rest have less than 20K.
It was a bit annoying at first as I wasn't collecting gems from mastering recipes and I have to go back and master those recipes but worth it in the end.