Chris,
Too bad that things didn't work out.
I have had primer issues also. I use Winchester LR primers and have had a few 360EX loads not fire, even though there is strong indentation on the primers. I attribute some of my failure to fire as perhaps the primer somehow got contaminated.
I have not seen much difference in performance using different primers. I use Winchester because that is what I could find. Previously, I used Federal primers.
In a different type weapon, I had the primer ignite but the powder failing to ignite. The bullet was driven into the barrel by the primer. Now that was my Ruger SR 454 and the load was 30 gr H110. I I am glad (lucky) I realized the problem before firing another round. I now use magnum primers with that gun.
However, with low pressure loads with the powder against the primer (held in place by the filler), I believe the issue is a primer issue. It sounds to me like there is inconsistent igniting the powder, giving inconsistent velocities. While I would think that regular primers would ignite your powder load, you might try magnum primers, just to see if there is a difference.
Now the main spring on some older guns will not fire magnum primers and one rifle I shot would only fire LP primers.
I don't use over-powder wads. I don't thing that the amount of powder that migrates into the filler is significant (if any powder does actually migrate)
I use a packing foam rod filler that is cut so that the base pushes against the powder and the top is at the case mouth. Seating the bullet compresses the foam filler.
Now, all that being said, the last time I was at the range, I got very inconsistent velocities with my Sherwood but fairly nice group. I was using 12.5 gr of 4198 which fills the case very well. However, with a long, skinny case and long stick powder, there could be an ignition issue.