I would suggest to turn the fan on to continuous run if it is a only use while you are working in the shop, when I run mine in the shop and it is cold the fan switch kicks on and runs for a few Min's and it cools off the heat exchanger so fast, that it shuts down the fan, thus the fan short cycles and all it is doing is heating the exchanger up and cooling it off, by turning it on continuously it takes the heat out and into the room until it can maintain the heat and the furnace cycles,
the make two stage furnaces now that use the valve to (guessing change pressure) to change the BTU input,
I do not think it would hurt any thing, (besides possibly stress the heat exchanger), but in the long run I do not know if it would help efficiency, my guess is if the fan is not continuous run that it would take longer to heat up the chamber to kick on the fan,
thus lower efficiency, (yes I know the furnace that is sized to heat loss that runs continuously is in theory the most efficient), but until is extremely over sized, I do not think you will improve it any by plugging off burners or orifices, if it extremely over sized, may be look in to the wall mount vent-less heaters, I have two thermostatic controlled units in the back rooms of the barn and (I like the infrared over the blue flame), there up to about 30,000 BTU,
I do not think you would do any damage to the furnace by plugging off the burners, but I do not think it would help you any either, (say it is a 100,000 unit and you plug off halve of the burners orifices, to make it a say a 50,000 input), but since ever other one of the heat exchangers vents are now venting cold air up it, I jsut do not not think the efficiency would be there, I think it would drop considerable, and if it was only 70% to start with it may drop to less than 50%, I think I would rather have it cycle, or find another furnace that is more closely matched. than try to alter, it. (altering it would lead to insurance problems as well if any thing ever happened),