Subject: Re: Exhaust Manifold Gasket
I just had my manifold off to replace the water jacket cover plate. When I went to re-fit it, the lugs on the bottom of the manifold fouled the new aluminium plate, which stopped the manifold going fully home. This was easy to spot with the engine at eye-level, so I just ground a bit off the bottom of the manifold.
Unless you have replaced the side plate it is difficult to see how this could be your problem, but I thought I'd mention it.
Another long shot - I don't suppose it's possible that the new gasket is thinner & the nuts are bottoming out before pulling the manifold home?