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What boost pressure are you seeing?
a hair over 3psi, dead on for the 3.36psi spring.

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.040 plug gap is a little big.
.035 should be fine,until you turn up the boost or run a lot of methanol.
Ok ill close them up a bit. I did inspect them and saw no signs of detonation on the plugs themselves.

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The valve out of adjustment issue?
How are you adjusting them?
Is it running rough?
I set them according to the motors manual on initial start up but they made noise, then we did a hot adjust on them, back off till they clatter, take the slack out and tighten 1 full turn. I still have a few 3 i think that are rattling loud. Im going to pull the cover again and see if maybe the lifters went dead?

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On the boost referenced Holly regulator, have you hooked up gauges to see what your fuel pressure is compared to you boost pressure?
What is your baseline static fuel pressure?
Something to check.
I have a gauge on the regulator itself, static pressure is 7psi, I will double check that its not leaking, maybe run a line and strap a gauge on the hood and see what its pushing under boost. Then again if it was a Fuel Pressure issue wouldn't the motor go lean? Im going to hook up the laptop and log the AFR's and post them next time im out.

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Do you have a choke valve on the carb, could be partially closing under boost?
Nope no choke, as for the tranny im going to pick up a pressure gauge and make sure its adjusted correctly sicne i had to make a custom mount for it. I really iwsh my buddy would break down and sell me his built 250, @ 3psi its hard to feel any significant power gains, i guess well see once i get the tuning down.