Help! Intake manifold won't fit!

It sounds like your old intake has been milled sometime before because of a possible head or block mill. Put the iron one on with no gaskets and then measure with two sets of feeler gauges on each side. Then do the same with the aluminum intake and see how much difference you have. And here is a good read for some other things to check and be aware of.
http://www.hughesengines.com/Upload/TechArticles/INTAKE_MANIFOLD_SEALINGJULY2015.pdf

Great call. I will do that and look at the article.