Have you started dialing in the outdoor reset curve yet? With the NHB boilers it usually does best on both efficiency & comfort by using the return rather than supply temperature for control, and tweaking the outdoor reset to the lowest temperatures that actually keep up with the load. Putting it in to return-temp control mode requires setting the first two positions on DIP SW 2 on the control board to ON (#1), OFF (#2). See p.48 in the manual.
Setting it up for cast iron rads with outdoor reset on high volume radiators read how to set up the parameters in section 9.6 (beginning on p.59) Set parameter A to "oRC" to enable outdoor reset mode control (page 59), parameter B to "6" for cast iron (p60). Parameters C & D will need to be tweaked experimentally to dial it in.
If you want use overnight setbacks you might want to set parameter E to speed up recovery from setbacks after the main curve is dialed in a bit.
You can probably leave the rest of the parameters at their default settings unless it exhibits short-cycling behavior during the shoulder seasons when the heat load is low (not very likely with high volume radiators and only two zones.)
With the reset curve adjusted fairly closely it will take a long time for the thermostats to be satisfied, and you can reduce the number of burn cycles per day to a mere handful. The house will stay at a very stable temperature, and the radiators won't change temperature very quickly at all- they'll always be somewhere between warm (or even tepid), and only get really hot when it's actually cold outside. The more time the boiler spends at return water temps of 120F or lower, the more condensing efficiency you'll get out of it. If it's been saving you 40% even without tweaking the curve in, it'll probably save ~50% with the curve tuned more finely, but as importantly, it'll stay comfortable, with no temperature over/under shoots from the burn cycles.