That sucks! Putting intakes on with the engine in the car is one of my least favorite jobs, especially with a cast iron intake - leaning over the fenders, trying to get it to sit right without disturbing the gaskets/RTV you've spent so much time positioning carefully,...
My only advice is if you've been doing this on your own, enlist the help of someone who knows what their way around an engine to help with the lifting, and perhaps instead of using all studs/nuts, which as you said may be interfering with how the manifold is sitting, have just a couple to keep the gaskets in place while you lower it on, and then use bolts for the rest?