So for emmisions all I need are the cat, egr and pcv valve. I'm not required to have the sniffer test, so could I build a nice engine and keep the stock intake with egr and just bolt it on once a year for the visual? Are there any negatives to the pcv? Thanks for any input.

You can run a vehicle without a cat and egr with no problem. I know from experience. I ran a full sized chevy truck for several years without a cat and EGR. The EGR was blocked off with a plate that sealed the hole. However, I would not run any engine of mine without the PCV valve. It keeps pressure inside the engine from building up. Internal pressure will certainly blow one or more of the following: Valve cover gasket, oil pan gasket, front and rear seals. It also prevents the oily residue from getting all over everything in the engine compartment by sucking it into the running engine and burning it.