Could I use Permatex gasket maker or something similar for the intake manifold gaskets instead of the stock mazda gaskets?

 

Yes, you could. I have used red RTV silicon before too.

 

I would not recommend it at all. Considering new replacement gaskets are only a few dollars, why go through all the work of stripping your engine down to the shortblock and not installing new gaskets. Also install new turbo coolant feed o-rings while you are at it.