Well Mike you might not have done everything you should have before the install, like a manual J, but that's a pretty nice install. There are two schools of thought here on the forum about boiler sizing. Size it for the typical load or for the worst case senario. You sized it for the typical load, not worse case. I happen to agree with that logic. Others will disagree. So you are actually heating 3,500 sq. ft. and domestic hot water. That's a good days work for the VF3000. I'm doing about 4k and it assists with domestic hot water. It struggles in extreme weather too. I keep my house at 68-70 degrees, also to keep wife happy. Woman have wacky thermostats. My wife is always too warm. Your mom is always too cold.
Not much can be done about that. I tell people we heat with coal and menopause.
The insulation sounds good. You should have the window conversation with dad again. Seventy five year old windows are not helping the situation.
I know many on the forum keep their homes quite warm. While I'm not crazy about 68 degrees, I find 70 to be quite comfortable. Keeping the home at 74 is part of the problem in my opinion. Maybe buy mom a really nice sweater.
Seven tons of coal doesn't sound bad to heat that much space and domestic hot water in PA. If that's his typical usage, I'm guessing he burned alittle more this year. This was an extreme year and everyone burned more fuel. Your settings sound right. Maybe the over fire draft is alittle strong. My over fire draft is .02 and I run the flue at .03-.04. Subtle difference but I think it makes some difference. I too run the combustion fan off of the distribution blower control. Mine runs 24/7 but on a reduced speed unless stoking. That helped me quite a bit.
I don't run my oil boiler at all. I could bring it into service in about 10 minutes if needed but I don't even have a vent pipe installed to avoid heat loss up its chimney. I think it's reasonable for most folks to have it setup the way yours does to kick on automatically. You mentioned having reduced water flow to the oil boiler. When the oil does kick on I assume that limits how much help its giving the VF3000. How much oil does he burn a season?
Of course your dad should be operating the cleaning rod regularly (couple times a week) to keep flyash off of the heat exchanger tubes, cleaning out the fly ash from under the grates and out of the vent pipes several times a season.
Your detectors are CO, not CO2. CO2 makes beer happy, CO makes you wake up dead.
Overall I don't think you have a problem worth installing a bypass. Since it perform wells 99% of the time and the issue is only during extreme weather, I would be happy. That's assuming he's not using any significant amount of oil. So really my advice would be to get mom a nice sweater, knock the heat back to 72 and convince dad to replace the windows. Remember free advice is worth just what you pay for it.