You're kinda right about the duct system being undersized: the system is undersized for the furnace, but the right size for the house (there's no humidifier, and the ducts and filter are absolutely clean).
It's really the furnace that's too darn big for the house. Every estimator that I've tried says 60K BTU is plenty for where I am and the square footage of the house, but the furnace itself is 90K. Either the geniuses at the so-called "professional" HVAC contractor didn't realize that central California isn't Minnesota, or this was the furnace what they had lying around. Based on the number of times I've had to crawl under the house to fix flex ducts that have come apart where they joined them to with "duct tape" that's dried out, either is a good chance.
The warranty has long since expired, so that's why I'm thinking about putting in the jets for 8000 foot elevation. I'm just not certain whether that will simply reduce the output (my hope), or if it will end up acting like an engine running too lean and blowtorch itself to death. Since my option is to fork out the money to buy a proper sized furnace, I'm thinking that modifying this one and running it 'til it dies is the best choice. Though I really hate abusing machinery that's the victim of a lousy sales and installation company.