Sounds like you have bent the rim
best to stick the remover in a vice and turn the wheel. Holding the wheel on the floor and using a breaker bar tends to torque the rim sideways.........
I exaggerated the length of the bar it was a section of old trampoline frame, it was about 12" or so.
What worries me is
I noticed when I built the bike when it was in the stand when i pedalled the freewheel seemed to rock up and down like it does now but I assumed this was because the bike was old and the freewheel was knackered. So when I fitted the new freewheel I thought this unevenness would go.
Kelly.....Body by Kona.............Soul by Satan !