With the engine assembled remove the valve adjusters from the rocker arms (identify them if possible and replace where they were).
Now all 12 valves are relaxed and fully seated.
All the intakes, and all the exhausts should be very close to the same height (but different intake vs. exhaust).
Any short? That's the problem valve. If it's an intake it may also be bent, and won't come out easily when head is off and the spring is released.
