Hopefully you've soaked the crap out of all the exhaust manifold bolts with some PB Blaster (or similar penetrating oil).
Before putting everything together, put the gasket up to the head and see if ALL of the ports line up correctly. Often times the gasket must be cut and each piece will need to be done individually. I used a little hi-temp RTV gasket maker to help hold the gasket in place while I fitted the manifold up. Also, try using the copper spray gasket maker on both sides of the gasket. It really seals up nicely so you won't get any exhaust leaks. And be sure to cover the exhaust ports up when you're spraying the heads.
Another thing, use some anti-seize on the exhaust bolts when reinstalling them.
Once you get it all back together and you fire the engine up, spray some soapy water over all of your exhaust piping and look for exhaust leaks, mostly around that new gasket you put in.