hip roof installation on a 2 story is always a troublesome installation. many folks make the mistake of setting the 10-2 based strictly on the roof they penetrate leading to down drafting on a consistent basis , the OP on the other hand has stood a higher flue up , but it still doesn't quite meet 10-2 on the second story roof, this results in an inconsistent draft. wind direction is the variable.
add the extra 2 ft if that will get you closer to the 10-2 for the second story ,or more if needed to get to that balance i'd start without the vacustack , if the chimney to roof height is proper then you wont need it anyway. seeing as the old 18-p from my company was downdrafting with its easy breathing ability , the stack may cause major downdrafting with the napoleon (not putting the "nap" down BTW , its a solid stove, just looking at the higher draft demand from the EPA stove than you are used to with the PRE-EPA Englander) the 10-2 is CRITICAL to get the stove to perform consistently especially with a less than ideal placement (not your fault) and the leaky house. stack effect is a major driver in your downdraft issues but the chimney can overcome it if its placed high enough in relation to the second story roof
add the extra 2 ft if that will get you closer to the 10-2 for the second story ,or more if needed to get to that balance i'd start without the vacustack , if the chimney to roof height is proper then you wont need it anyway. seeing as the old 18-p from my company was downdrafting with its easy breathing ability , the stack may cause major downdrafting with the napoleon (not putting the "nap" down BTW , its a solid stove, just looking at the higher draft demand from the EPA stove than you are used to with the PRE-EPA Englander) the 10-2 is CRITICAL to get the stove to perform consistently especially with a less than ideal placement (not your fault) and the leaky house. stack effect is a major driver in your downdraft issues but the chimney can overcome it if its placed high enough in relation to the second story roof