I sought out a post like this for a reason.
If a car is losing boost with freer-flowing headers, it may be the case that the valve timing itself is partially to blame, for not being optimized for cylinder fill with a less-restrictive exhaust system.
The stock headers are coupled with the stock valve timing.
If, for example, the exhaust ports vented to a perfect vacuum, you would not need as much exhaust timing, because you would be discarding fresh air, possibly with some gasoline, out the exhaust port during overlap.
The closer your exhaust port approaches a perfect vacuum, the less exhaust valve timing you need, especially during the critical overlap period.
Ironically, adding a turbocharger ALSO lessens the need for exhaust valve timing, because there is so much backpressure that having the exhaust valves open a good, long time will get you far more reversion than with a system vented to atmosphere without a turbocharger intervening.
The most timing, intake and exhaust, will be for n/a engines.
I would think that cam specs for very high-flow exhaust systems, most specifically, large-tube headers, should have less duration than cams for exhaust systems with somewhat shorter and more restrictive headers.
In FACT, since the blower acts as somewhat of a one-way valve, I think it would pay off to experiment with truly oversized (to the common mindset) headers, to take advantage of that, so that the initial exhaust rush would have a nice, big, low-restriction chamber by which to exit. Now, obviously, at lower RPM, where these engines need literally NO HELP WHATSOEVER, PERIOD, FULL STOP, you may lose some power due to somewhat reduced scavenging by the exiting exhaust gas "accordian" not stretching as far as it does with smaller-tube headers, but, hey, why not have dual-chamber exhaust primaries? It works well on intakes, such as the original Corvette ZR-1. It would not be rocket science to set it up. a butterfly positioned so it shuts off the secondary exhaust primaries could open to reduce resistance at higher RPM and tune the "accordian efffect" such that it would be optimized at its target RPM.
There is only so much magic that can happen with the same pipe serving all RPM.