Hi msr57965,
Are you still having issues? I repair shipboard gas compressors for a living; maybe I can be of some assistance. Please let me know if this is indeed shipboard.
It's certainly possible for the axial runout to be the cause of this issue. Often times this is because the bearings...
What kind of environment will this be in? Is this a one-off part or will you be making many of these?
An o-ring is certainly a viable option and so is Permatex and Hylomar.