Damn, that sucks. The other gasket fit just as bad? Problem with not having a gasket in there could cause a clearance issue, not to mention that's a lot of surface area to try to seal with a liquid gasket, any leaks in the crank area and you're scewed.
For the studs your going to want to install heli-coils in the cylinder and then re=install the studs. The black box is a boost bottle, you don't need it but you don't want any air leaks in your intake.