I plan to replace the heads on my current engine. I am running the crossfire set up and will retain them. I plan to modify this set up. My question is the after market alum heads have no provision for the egr,will the intake (crossfire) still function ok. Is there a gasket that blocks of the egr passage or just run oem or eqiuvalent?

You can block off the EGR opening. Get a new gasket and use it as a template and cut it out of 1/8" alum. Bolt on with gasket in place.

The rims depend on the tires you put on them.  If the overall size (tire height and width) is the same, the rims will be fine.

Here is a place that makes a performance cross-fire intake manifold that might enhance the performance of the aluminum heads you are putting on.