this may sound crazy but you know what I'd try, I'd punch a small hole in the valley pan close to the suspected offending cyls & shoot some starting fluid in there with the straw to aim it close & see if it straightens out cuz if it is a vac leak its highly likely that it could be on the bottom side of the valley pan which is why it ain't showing up being sprayed on top. EDIT I reread & you are already all apart so in that case I'd go ahead with paper gaskets as is or milling and gaskets but I would mockup right now to check the alignment plus have the shop check the intake. Sounds like the down time is adding up