Just a final follow-up... the wefixhvac guy was top notch, I highly recommend him.
The first guys (theboilerguys) left the pilot line loose (more accurate, not tight enough, I ended up finding and fixing this myself...) and also put the burners back together crooked (not a functional problem, just sloppy). The main gas leak was the line they did not properly tighten. There was also a small secondary leak from the gas valve inside the boiler (not their fault but they also did not notice it during service). They also did not notice that the circulator pump was seized and that the water input valve was stuck open. Basically they missed all the problems (stuff that they should have caught and stuff they would have made extra money servicing/fixing), created some new ones and charged me a couple hundred to vacuum out the boiler...
All is fixed now (new pump, new gas valve, everything properly put back together), we have heat now in rooms that were always cold before (some end of line rads were not getting hot due to the seized pump). The system works better now than it ever has for us. I am interested to see how our gas bill changes...
Thanks to mimico_polak for the recommendation. The wefixhvac guy really knew his stuff and spotted all the problems right off!