Sounds like the overshoot is more of a thermostat issue- if you can narrow up the hysteresis delta on it you'd get shorter burns but lower temperature swings. Since you're burns are measured in HOURS, I'm not too worried about short cycling the thing. If all else fails a PID-algorithm Tekmar thermostat would deliver extremely tight room temperature control.
A check valve on the condensate pump is one thing, but the drain trap something else. There needs to be liquid in the trap for it to function properly, and when the boiler is idling or off all summer the trap will dry out unless it has a regular source of water from somewhere else.