Simply employing a stock block would not make anything stock.
Those cars have the stock engines. Really. They have the stock internals, in a stock block, with stock heads, stock lifters, rocker arms, valvesprings, stock intakes, stock throttle bodies, and stock engine management.
In regards to the pulleys and CAI, answer me this: If you simply removed something from an engine, would that mean that the engine is not stock? Let's say that I simply removed the air silencer, or took off the stock air box. I haven't touched the engine, all I've done is allowed more air into it. The engine itself is stock. If I removed an accessory such as the air conditioning or smog pump, that's not part of the engine. It's attached to it, but it's not part of it. Removing those two items would cover the amount of power that you would gain from pulleys. Still, the engine itself is stock, never been cracked open or messed with, just the accessory drives and the air that passes through the mass air into the throttle body.
I would still consider this a stock car. Also, simply taking stuff out of a car, like the spare tire and jack, or rear seat, does not mean the car isn't stock, at least not in my eyes. But I understand that that is debatable.
I agree with you about the suspension components though, those are not stock items. I thought you were referring more to the engines in your original post.