"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).