RTV in the corners of the LIM are there to seal the block end seal to the actual lim/head gasket. All it does is keep oil from seeping out of the valley area. This will probably seep and cause you to want to redo the gaskets, but not cause an engine running issue.

Did you burp the cooling system? That is a common issue when you mention the hoses are not firm. But that takes some running time.

Check your vacuum connections. Did you replace all the gaskets and clean all the surfaces well?