How does cid make power?

This doesn’t explain why so many strokers are giant underachievers.

Sure it does - stroke isn't the best way to get the CID, it's just the only way left once bore is at max. The engine will still make more power, just not as much more as with bore. An increase in bore size will pay off to a much greater extent since piston area increases with the square of the radius.
Also, the piston speed is higher with a stroker which would suggest the need for an over-capable head. Piston speed obviously has an effect on how fast the engine is trying to move the air through the port and past the valve. Trying to feed a bigger motor from the same tiny ports is always going to pull the peak rpms down. Most folks don't even want to play with offset rockers, so it's no surprise most strokers run out of huff over 5500.
Look at 410 sprint motors - they're running near a 4" stroke, but much larger bores (4.1+). They wind out past 8k and make over 800 hp as a result. The biggest difference between a 4.04x4 408 and that 4.13x3.8 410? The 410 heads flow 400+ cfm. Sure, the smaller bore won't make as much as the bigger, even with those massive heads - but the better heads would damn sure feed the 408 better than any over-the-counter head on the market today.

Look at the PONTIAC. Long stroke tractor engines. Ou can make 600 HP at 5500 but it wold get killed by 600 HP at 7000.

Sounds like the same issue as above. I suspect Pontiac gets as much love from the aftermarket head guys as MOPARs do.

Edit: 7000 is NOTHING with today’s valve train components.

Only applies when cheap-asses actually invest in good valve train ;) Most guys don't, then whine about underachieving results. Just look how many people shy away from doing any B3 type corrections to their heads - and all the guys who do tend to have better results.
Similar for custom-ground cams. Ramp rates should have some relationship to total lift AND geometry, otherwise losing valve control can happen super early. But that applies to all engines independent of CID. It's just that to get larger strokes to breathe better, it requires more of everything to run 'right'.