There are a few things you can check. The heater system is really quite simple.
First, when engine is warm, check to see if BOTH lines in the firewall (input and outgoing of the core) are warm or hot to touch. If both are hot, core is not clogged. The coolant is going in (one hose hot) and coming back out (second hose hot).
If only one hose is hot, core is clogged. Get an old garden hose (or and old washing machine hose--cut one end off--hook the washing machine hose to your garden hose) and attach the cut end of the hose to your core hose---you can unhook both lines going into your firewall where they attach to you enginer (intake). Get a two inch piece of copper line or other little tube to hook the garden hose to the core hose.
Unleash the dam!! See if junk gets spurted out the other line.
If you use an air compressor, do not use too much pressure--maybe 40psi max...you can damage your core and end up with a lake on your floorboard.
If core is not clogged (both lines hot), your heater doors (flaps) are not opening/closing correctly. cables attach to these doors to open defrost, heat, vent, etc....
You mentioned you replaced your thermostadt, therefore, i dont think it would be the coolant not getting hot enough---that should be fine. Is your temp sensor guage coming off the lowest setting after 10 minutes of running? If it moves suddenly, that is when your thermostadt opens and all is working well there. You mentioned it gets warmer when you are idling at a stop....that is because no cold air is forced through the radiator to engine and it should be warmer. You can always do the old school bus trick and put some cardboard in front of the radiator in your grille. That'll get her warmer.
I dont thing air bubbles are a problem as long as your coolant level is fine and your radiator cap is relativley new......people often overlook replacing radiator caps w/ normal preventative maintenance....they have a spring coil that opens up when it gets too hot (lots of pressure) to let off steam/coolant into your resevoir. Replace your cap atleast once every other year or when having troubles with coolant level/heating system.
hope this helps
SgtDel
aka "Andy"
www.delbridge.net
1979 Big 10 383 stroker
1991 Blu 'Burb 3/4 ton 4x4