I am wondering whether the leak was there from the start, as an assembly fault, but only increased after fitting the filter. If the filter was fitted in the return line to the tank after the feed to the rockers, any restriction by the filter will tend to send more oil back to the crankcase via the rocker feed, and this oil will continue to build up. Simply removing the filter element will eliminate this factor. Any oil accumulating in the sump will tend to increase the crankcase pressure and this may have displaced the crank seal. I always use two circular gaskets, one each side, to seal the spacer between the crankcase and the primary inner case. As long as there are no missing bolts or other holes between the case and the crankcase, the primary should remain dry.
All these should be in order on a newly rebuilt motor. The leak may actually be a consequence of some assembly fault, introducing too much oil into the crankcase, or a failure to scavenge correctly. Plus any aspect of the breather assembly which prevent its correct operation. If it runs ok with a tappet cover off, suspect the breather.
Swarfy