With 45 minutes on, 5 minutes off, it's running a 90% duty cycle at an outdoor temp 6F below your 99% design temp, which is 112% of the design heat load. That's about as good as it gets for right-sizing- it means it would still keep up even at 0F. With further weatherizing you'll quickly gain even more margin.
But right-sizing means deep overnight setbacks will have long recovery ramps. One way to deal with that is using a "smart" thermostat that "learns" your system and temperature preferences, and adjusts the timing of the recovery ramp to compensate for the outdoor temps by modeling how long it has taken to hit the setpoints on recent calls for heat, including how long it takes for maintenance burns on at the setback setpoint. There are a number of them out there- the smart-phone fans all rave about the Nest (first among several wi-fi enabled thermostats), which can be monitored & controlled via internet if you like, but it also learns pretty quickly what your normal use patterns are. It's a $250 thermostat, but very slick, and many utilities offer rebates on them- not sure if your gas supplier in Smithtown would.
In a well designed decently tight home the thermal mass of the house and the excess BTU output of the heating system above the current heat load is what determines the ramp rate. As you improve the thermal efficiency of the building envelope two things happen: The cool-off rate slows to the point that you don't always hit the setback temperature, and you have more excess output to heat up the thermal mass of the building and it's contents. It doesn't sound like you are radiation-limited- it's delivering the whole-shebang of what the boiler is putting out, so spend the time and money on the thermal envelope of the house, starting with air-sealing.
If your basement if 50F even with the boiler running a 90% duty cycle with uninsulated heating plumbing down there when it's +9F outside, it means you have significant air leakage into the basement and no foundation insulation. The air sealing aspect is extremely low-hanging fruit, but the foundation insulation may be more cost-effective than adding more insulation to the attic, assuming you have at least 5" of fiber up there. (The attic insulation would still be cost effective though.) Air sealing the band joist and foundation sill is huge- it's often the largest air leak in an otherwise middle-of-the road leakage house, and more than all of the window & door crackage combined. Air sealing at the ceiling plane to the attic paying close attention to any un-sealed electrical & plumbing/flue penetrations that extend from basement to attic, as well as all of the light fixtures, and access hatch weatherstrippping would be critical first-steps prior to adding attic insulation, otherwise the now-colder attic would be far more susceptible to mold/rot issues from air-transported moisture in winter.
I have retrofitted ~R18 in rigid foam on my basement walls and air sealed most of the foundation sill & band joist- it never dropped below 64F in even when it was -4F out recently, even though I let the first floor drop to 60F during setback, which it DID hit, according to my various temperature & humidity monitoring meters that log the extremes.
In a well designed home (or a crummy one) the time to heat up is a function of the temperature rise and the thermal mass of the house, relative to the excess BTU output of the boiler above the instantaneous heat load. You can either spend your money boosting the output, or on lowering the load, but lowering the load will provide more comfort, and is the better long term investment.
With 45 minutes on/ 5 minutes off during a recover ramp you're running a 90% duty cycle on the boiler, at an outdoor temp 6F below the 99% outside design temp, which is 112% of the design heat load in your case. Kicking on the second stage would not increase the recovery ramp rate, only the frequency of cycling (=bad for efficiency and wear/tear on the boiler.) With your existing radiation running on just the first stage you're good to at least 0F before it loses ground, since it's actually heating, even recovering at a 90% duty cycle. That means you're already above 1.3x oversizing (which would be a nearly ideal oversizing factor, if the 90% duty cycle was at a steady state, not a recovery ramp from deep setback.)
Adding more radiation will not improve the ramp rate unless you added a LOT of radiation, to be able to deliver the lions-share of the increased output of the second stage. Reducing the heat load would improve the recovery rate substantially, even with the existing radiation, since the excess radiation output above the instantaneous load would be increased. Raising the high-temp limit to 200F would give you both a higher output, and a higher duty cycle, so start there, and start working the building envelope issues...
...beginning with air-sealing: If you add insulation without air sealing you'll increase the risk of mold from air-transported room-air moisture getting into the walls and attic. The band joist and foundation sill leakage is likely to be the single largest air leak (which is why it drops to 50F downstairs), but in a raised-ranch it could also be substantial air leakage at the cantilevered overhangs. You may be able to figure out where the most egregious air leaks are with the IR thermostat, especially if you de-pressurize the house a bit by turning on all of the bath/kitchen exhaust and turn on the clothes dryer. (Even smaller leaks are easy to spot with infra-red cameras and a powerful blower door test, but start with the big leaks.) The upper floor ceiling plane is most-critical, for air tightness, followed by the lowest level leaks in the house at grade, since that's what determines the "stack effect" pressures driving infiltration.