Okay, so we all know there are several major bugs with the furnace and smelting, but after messing around with things and babysitting my ore haul, I discovered a workaround for the furnace consuming too many ore with stokes remaining.
How it works is similar to the trick where users keep one piece of expendable ore to drop whenever their furnace fails to smelt four ore into one bar. After losing countless pieces of gold ore making five-ore bars when my furnace should have been making four-ore bars, I decided to keep one piece of expendable ore (anything of a lower quality) per complete set of four gold ore.
In the test run I just completed, I had mined twelve pieces of gold ore, good for three gold bars, as well as plenty of rubies and moonstone shards. With my mining complete, I returned to the furnace. I had five stokes remaining, but I knew that because I had rubies and shards in front of the first chunk of gold ore, it would most likely try to consume five gold instead of four, as it tends to do when mining gems or shards before a set of metal ore. To prevent this, I waited until the gems and shards in front were smelted, and when my gold reached the first slot, I dropped one of the extra pieces of silver. The furnace immediately acted as though I had no stokes, and I had to restoke it for 1,000 Pebbles. Thankfully, it produced one four-ore bar of gold!
I repeated this process, waiting for my gems and shards to smelt until a gold ore landed in the first slot, at which point I would quickly drop a silver ore and stoke the furnace for 1,000 Pebbles, close the error window, and refresh the page. (Note that the number of stokes would count down normally from wherever it left off. I technically started with five stokes and ended with two, showing that only three were consumed for the gold bars.) This successfully gave me a four-ore bar of gold each time, wasting none of my gold ore by ignoring the stokes. You can, of course, replace the gold with whatever ore you're mining for, and the silver with whatever lower grade metal you're comfortable dropping. Just make sure you're quick while dropping and stoking to avoid wasting/missing anything!
Apologies if this isn't the correct place a full bug workaround. I just thought this would be the best place for people to see it if anyone was still having issues with this! Also, I apologize if anyone else posted this full workaround previously. I hadn't seen anyone describe this in detail before past the "drop one piece to smelt four leftover ore" trick, so I thought I'd share.