I believe it is because of the firing order, on a Chevy six the front most cylinder is #1 and the rearmost is #6, going up in order, the firing order is 1-5-3-6-2-4 so when split up in 2 headers there is no cylinders that share a header that fire back to back, whereas with a common header/manifold there is always a pulse from the last fired cylinder, I'm sure the cam overlap has some part into it too with the lack of scavenging to muffle it or something
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So ideally, a Doug Thorley tri-y style header would be best. Although, like you said, take the front 3/rear 3 dual into a single for better scavenging effect, that may be easier. I plan on doing the lump upgrade, HEI, and dual exhaust into single at the very least. The lump upgrade alone increases the torque a lot over stock. And that's why I got this engine, to have torque.
I also want an Offenhauser intake to run dual carbs, or an intake to run a q-jet. Simple upgrades that make the engine more efficient.
Going through my '63 shop manual right now, and these engines really appear to be easy to work on.
Compression is supposed to be 130. If that is all within 20 psi on each cylinder I may just check the main bearings and rod bearings, reseal it and run it.
Adjusting the valves is similar to the small block with hydraulic lifters, where you find zero lash and turn 1 turn past zero lash.