Love the car.

I'm not sure I understand the question about pistons. Piston manufacturer specifies a specific clearance at a specific measuring point on the part. Typically the clearance is achieved right at the specified bore diameter the pistons were built for.

If you really think the pistons are stuck in the bores......Get it good and hot, put on some welding gloves so you don't burn yourself, pull all the spark plugs out, put a breaker bar on the damper bolt and see how hard it is to turn with a bar.

"it does not want to run, and when it's at a stoplight it stalls"

When that happens, Does the starter work okay, does the engine spin relatively fast when you turn the key?
If it does, it's not piston to wall clearance.

It's hard to tell by the pictures, but if there were a major problem with clearance, the pistons would be visibly damaged and it doesn't appear they are (from the little bit that is visible).

Lots of things it could be, ignition, fuel, vapor lock, a ground or connection that goes bad when it's hot, stuff like that.

When he swapped the intake, did he block the heat crossover?