Replaced axle and now clunking in back 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.
You should ensure the outer races of the hub free of pits and corrosion. The wheel may feel smooth when spinning it off the bike, but the roughness may appear only when the bearing is loaded.