Why did you rebuild the forks? what did you do?
Was this problem there before the rebuild?
Are the fork springs new, or new the this motorcycle?
Typically that spacer is somewhat cone shaped and slides over the end of the damper rod. If that is the type you have, and most older forks were made that way, I don't think you could put it in upside down. I don't think the damper rod bolt would be any where long enough to reach the damper rod with the spacer in upside down.
You say you have no sag and the fork tops out, if the spring is new perhaps it is the wrong one, much to stiff, and just overwhelms the damping force and top out springs.