I finally got a rear axle replaced, and all new cones on a new axle... I assembled it back together with 7 or 8 of the bearings in on each side and some grease, put it all back together, put the freewheel cogs on (how did I even try it without the freewheel remover before...) and wheel was spinning fine without play left/right (well, maybe 1mm). The gears all shift too.
When I ride the bike I am often hearing a clunking in the rear though. When I just spin the crank or wheel when the bike is stopped It seems I cannot get it to happen. The back wheel feels pretty good. What should I look at for adjusting this? It happens when freewheeling and when pedaling and I don't see anything obviously tapping or loose.