What I suspect is that when your boiler is running it is managing to get just over the bottom thermal and time limits needed for the exhaust gasses to burn off the coal tars and related materials so up to now you have been lucky and have not had any problems. You drop below that point and you will start getting exactly what I described.
I honestly cannot see how you can come to the conclusions that your concept is a good idea since the very operators manual you posted clearly states that pretty much everything you are doing is wrong, dangerous and just a bad idea in general.
No boiler system should ever controlled by the stack temperature because stack temperatures have no exact correlation to water temperatures and heating times on a properly functioning system.
The stack temp and water temperature are not directly proportional and the burn rate VS temp change relations can be drastically different with very small external changes in working parameters.
What exactly are you thinking this will do to your advantage?
I guarantee it wont save fuel but it will create more problems than you already have at some point.
I have strong suspicions that your heating system is possibly badly designed, improperly sized, or missing its true and correct control systems and critical components as per whats suggested in the manual.
Plus I doubt it is presently up to code or meets insurance requirements and regulations if your even insured at all. If it is up to code and meets insurance requirements this design change will void any of that.
Without more explanation as to how the system is set up and how its being used I can not come up with a valid reason to think that this is any form of safe heating system to be using. Its just a disaster waiting to happen.