I don't know if you found your problem, but it sounds like what I ran into with an HEI dist in my 292. I already had an HEI in the engine, but I ran across a couple at the wrecking yard and grabbed them.
I can't post a picture because of the photo image police, so you'll have the click the link.
The one on the right is an external coil unit out of a '75 Nova 250, but unfortunately it has the flex joint shaft and I will probably never use it. The second from the right was out of a mid-size Buick with a 250. Next is a stock 250-292 distributor. The last one is a Corvair dist, which is close to the same, but with a longer shaft.
Distributors The last image is the shaft of the Buick unit that is .025" smaller, below the gear. With the gear in place, you can not see the difference. I had put it in my 292 and it wobbled, just as you described. As you can see from the first image, you can't tell the difference for looking.
250 shaft
