Sometimes a freewheel wobble is caused by a dork-disc that is seating only part way around the hub/freewheel interface, due to the hole in the disc being big enough to pass freely over the threads (i.e. too big to reliably self-center).
Ditch the dork disc (if present), if only to test for this possibility.
And try the freewheel on a different wheel, since Shimano freewheels typically show very good manufacturing consistency.

I've seen rear hubs that got bent between the left and right flanges, either from wheel impact or from careless spoke tensioning sequence.
Do the two flanges spin perfectly true(?), they should.