With the basement insulated it's more relevant to use the DOE output, not the IBR-net numbers, since the standby & distribution losses are still indoors, and actively heating the first floor. (Think of the distribution plumbing as a long skinny radiator. ) For your boiler that's ~140,000 BTU/hr.
A decently insulated 2x6 1.5-2 story 4200' house with at least R20 in the attic and clear glass double panes (or clear storms over single pane double-hungs) and an insulated basement would come in with a heat load of about 50,000-80,000 BTU/hr @ 0F, and proportionally less at +10F (or whatever your 99% outside design temp happens to be.) So you're probably in the 2x oversized range for the whole house load, which isn't terrible, if less than ideal. ASHRAE recommends 1.4x oversizing factor of the 99% load as the best compromise for non-modulating boilers.
The 100' of baseboard on the first floor can deliver about 50,000 BTU/hr of heat at a boiler temp of 180F. It probably doesn't need to be that high, but both zones 1 & 2 together only add up to a bit more than 1/3 of the boiler's output. Even adding in the 50' for the third zone you'd be at only about half the boiler's DOE output, so yeah, it's doing a lot of unnecessary cycling on zone calls AND for the whole house load. With an indirect water heater zone as the "priority zone" the biggest boiler that should ever be hooked up to 150' of baseboard would be about 75-80K of DOE output. That's enough burner to deliver a continuous full-flow shower, and unless you're showering for an hour at a time you'll never miss the drop-out of the heating system when it's serving the indirect.
Annual fuel use numbers aren't really very good for estimating heat loads without using a more sophisticated boiler model. There is a lot of error related to hot water use and solar gain in the shoulder season. Mid to late winter fill-ups reflect a higher duty cycle, low solar gain, and a lions share of the fuel going toward space heating. So if you have some K-factors or billing slips from the mid-winter to at latest April Fools day we CAN figure this out. With only 75,000 BTU/hr of baseboard and some standby/distribution loss heating it's pretty clear that the whole house load is no more than 80K, but it could be only 60K (even when fully heating the upstairs. When dropping the temps upstairs your oversize factor is probably going to be closer to 3x than 2x.
Given your limited zone radiation it's worth retrofitting a heat purging boiler economizer control (eg
Intellicon HW+ , there are others) and setting the low-limit to 140F (any cooler and it risks copious acidic exhaust condensation in the flue). This type of boiler control maximizes the use of the available thermal mass in the system & boiler. On a new call for heat it purges heat from the boiler until it hits the programmed low temp, but allows the high temp to run as high as it needs to. When it "learns" the system based on recent burn history it anticipates the end of a call for heat cutting the burner early to park the boiler at a lower temp between calls for heat, thus reducing standby losses. Between the reduced number of ignition cycles and the lower standby loss the overall burner on time will in your case likely be cut by 10-15%, possibly more.
Many/most new cast iron boilers come with heat purging controls, ever since
this bit of research at Brookhaven Nat'l Labs was published about a decade ago. See Table 3. At an oversize factor of 2x most boilers run 5-10% below their AFUE numbers even without the short-cycling issue. System #3 was the only one with heat purge control that was tested, dropping only 1% in as-used efficiency even at an oversize factor of 3x.
The fact that the basement cruises along at 68F indicates fairly high standby & distribution losses. A heat purging controller will reduce the basement temp by a few degree too, which lowers the actual heat loss. (You don't really care if it's 65F down there instead of 68F, do you?)
Is the air conditioning broken up into zones? Is it recent enough to use R410A refrigerant, not R22 or R12? Are any of the ducts or air handler on the other side of the insulation, say behind the kneewalls? (Sounds like it might be if it's cascading cold air onto the thermostat.)