Thanks for all the responses...
The misalignment I was talking about was side to side. Fore and aft is fine. The other thing that bothered me is that the left stick contacts the edge of the opening where the stick emerges, when deflected full right. It touches about the same time as the control hits the stop, enough to wear the paint off the weldment.
Anyhow, I removed the cover under the seat today and readjusted the push rod ends so that with the flaperon mechanism locked in place with the locking bolt, both sticks are vertical within a degree. That satisfied my sense of athetics. However the left stick still contacted the edge of the opening with full right deflection. Called Van's, and they agreed that that is not desireable and agreed it would be permissable to file off 1/16 inch from the side of the metal opening, which I did.
I think the issue was probably due to a slight variation in the stick weldment. Anyway, problem solved. I repaired the paint wound with the weldment touch-up bottle from Van's.