I recapped it. It fixed some display linearity problems, but it was plusing the focus a bit less. I dug out another 4600 chassis that was working a few weeks ago, swapped the flyback, and it had no video.
So to check if I messed up the main part of the original chassis, I put the orignal flyback back in and now its pulsing the focus more than before. So shaking it up a bit during the transfer made it worse.
I am going to put back together the spare chassis to see if its still working. I will dig out another tube and try testing the 4600 chassis in that.
update: After fixing another 4600 chassis with similar results, I dug out a 2nd 4600 tube. Problem is in the tube. When re-checking the neck for a bent pin, I found the ground pin loose. Tube socket was holding it in place.