Am I correct in assuming when you replaced the Taco circulation pump that you did, in fact, only replace the motor and you did not have to open the system and drain the water?
How long has the system, especially the 2nd floor heat, been working satisfactorily?
If you explore the second floor baseboard loop, you should see where the water comes up from the basement and then returns back down. Look for the return to the basement (usually at the end of the floor loop) and you should see a bleed valve at that elbow. You may have to remove the baseboard cover.
Get a bucket and bleed all the air until you have a steady flow of water and hopefully that will fix the problem. You might also check the head pressure as indicated on the gauge at the boiler to make sure you have the correct pressure in the system.