Is the EGR still required if I upgrade the intake manifold to a Marine intake or a Stealth ram intake? I am asking if it is needed to pass emissions for CA smog. Do I have to reprogram the ECU?

 

If the point is to pass CA smog, the whole thing is technically illegal.
The CA smog open EGR full-duty cycle to test functionality as far as I know. If you want a shot at passing smog make the Marin manifold as close to stock-looking as possible and think about retaining EGR. Without EGR you have no chance of passing CA smog.