Your advice was well-taken.
I had the duct cleaning folks come in yesterday, and it was AMAZING what they did. Cleaned all the ducts and patched/replace the ones that had problems. That was what I expected.
What I didn't expect was they removed blowers from both furnaces, completely cleaned them and completely cleaned the furnace itself, the returns, and the vents. Our furnaces now look like they are straight out of the box. I am sure the air we are now breathing is much cleaner.
In that regard, we replaced the cheap filters I had installed with MERV 11 ones that I got from Amazon. They are still one one inch think (not the massive 5 inch thick MERV 16 in my OP), and they should be pretty fine. It's very hot in the Bay Area now (nearing triple digits) and very poor air quality because of the smoke from the fires. However, although we have the windows closed, we are now using the fans from the furnaces without the heat to cool the house down along with a few stand-alone fans. It's working fine. I only realized a few months ago that you could use the furnace fans without the heat to cool the house down. I also checked with our main HVAC company, and they say it's perfectly fine to let the blowers/fans run constantly, which we will do for the next several days with the excessive heat warning and the smoke. Apparently, the greatest damage to the blowers comes when they are turning on and off.
Also, buy your air filters on-line, not at the store. You'll get a much cheaper per unit price and a better selection. I'm going to use this and see how it goes now.