How exactly do you get all the air out of a hot water system with gas boiler?
Keep on allowing the water from the supply line run through the lines individually and opening the purge valve on the return. And the pipes continue making noises (knocking)

On mine, I remove the baseboard radiator cover, at one end of the radiators is a vent valve. Some require a screw driver others require a special tool. In mine I let the furnace heat up somewhat then I have pressure in the lines to bleed. I open the bleeder valve and catch water in a botle. When I get a stead stream without air close the valve. This can be done at each room.

Do as paratechs says, bleed each register. Also, can you tell us if this noise is constant whenever the boiler is running, or does it only occur when the boiler first fires up, and again when boiler shuts down. Often times, the KNOCKING noise you are hearing is the expansion of copper pipes againts wood joist(caused by being to tight to wood), if this is the case, it will only happen as water is heating, and again when water is cooling. Usually, air in the system will not create a KNOCKING sound, but more just an annoying water air flow sound(cant think of the word to describe it right now, ugh) only at the register.

Basically, turn your themostat way up, let the system run, and tell us if the sound is constant for an hour, or if it is only for the first five or ten minutes, then goes away. If it goes away, turn the thermostat back down, and let us know if the knocking starts again,, if it does, your problem is not with air, but with expansion and contraction of heating pipes against wood surfaces. Hope this makes sense. Lee.

Lee... You sound more knowledgeable tha I about boilers. Can you respond to my post... I have a Weil Mclaine boiler. I brush it out annually then pull the burner and sweep out the debris that falls into the fire box. Each year the liner (wet pack) has more areas of cracking or concern. I found the replacement part numbers but how do I install the pack? Do I simply wet it and place it. Do I somehow glue it in? I am referring to the floor and rear refractory.. maybe even the front also. I have had the boiler apart but have not removed the old pack or ordered the parts yet. Product diagram http://www.weil-mclain.com/professio... ntinued/68.pdf

Sorry paratechs, I have not had any experience with replacing this item, but it should give you thorough instructions with the kit. Please let me know more about it when you get the kit, always interested in learning. Sorry I can't be of further help with this. Lee.