At the very least you have a partially or fully plugged up heat exchanger, and at the worst the secondary is also in the beginning stages of plugging.
The yellow flame means there is not enough combustion air mixing with the fuel to burn correctly. Yellow flame equals excess carbon which is what is plugging up the heat exchanger blocking yet more airflow creating more and more excess carbon. Left unchecked this thing will plug totally or hopefully open the pressure differential switch and shut the system down and lock it out.
You must get a qualified service tech on this issue as soon as you can, it may not be too late to have a reasonable repair cost...but trying to operate it much longer and you can kiss goodbye just about any money the high efficiency has saved you for the last couple of years !!!!!!