Spend minimal effort thinking of any of this for now, and focus on finding a clean shell with minimal rust first. Take it from someone who's had to go through it a bit and had to do a lot of work twice... just pay more up front for a cleaner starting example. Fortunately you have more of those in California.
Once you have a clean car I would focus on brakes and suspension before swaps. Once that's done you'll quickly get an idea of how much things are really going to cost you down the road.
Smog laws will affect your options in CA unless you plan on buying a California EO approved Chevy crate engine if you end up with a later car. LS with a 6 speed and low gearing, or an SR20 will get you the best fuel economy compared to other options if you actually care about that sort of thing.