Do you use the factory specifications if you have aftermarket camshafts installed? If not, how do you figure out the gap to use? I'm assuming you don't use the factory specifications(?)...maybe add or subtract the difference in lift from the stock ones??
Factory specs should be okay. I don't see any reason why you would use other specs. You might go a thousandths of an inch tighter, but I would just stick with stock specs.
The only thing you might have to take a closer look at is the position of the cam when you check the valve lash. Make sure you are measuring the distance between the valve rocker and the base circle of the cam. You don't want to measure the lash anywhere except the base circle.
The method I use which I would only recommend to knowledgeable people is to turn the cam so that you KNOW you are on the base circle. This means that you want to turn the cam further into the power stroke for the intake, and further into the compression stroke for the exhaust (basically just before or just after TDC). I find that as much as 20 degrees on the cam is needed to insure that you're well into the base circle.
I think the factory specs are set intentionally loose due to Honda's wide duration and the fact that it is nearly impossible to get them set properly using the marks on the cam gears.
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