That wasn't really the question, was it? Only a matter of whether it will or won't fit. But then you raised the question of power output when you said:
...which asserts that a PowerBomb is factually inferior in some way to the stock '08 header, an assertion for which you offer no support. You do mention that you have run the '08 muffler with a PMB cap, and that should remove the second, more restrictive, of the two cones in the core, and evidently, you were happy with the improvement. I'm not surprised. But, you fail to note whether you have run any other header with that setup, so from your experience, at least as presented, we can't tell whether a different header will accomplish one thing or any other.
...why down grade?
My experience with PowerBombs has been that in spite of any claims to the contrary, they don't really add a significant amount of power at peak, but rather, they have the tendency to flatten the torque curve and broaden it because the engine "sees" them as a header without a particular fixed length. They are very effective on engines with a pronounced "hit", as they work to smooth that out by spreading the power downward from that point in the power band. So given the OP's remark/complaint regarding the bike now behaving like a two stroke, I'd have to guess from experience that it would be helpful. Then again, so might a stock '07 header, for different reasons.
The statement you made regarding header volume:
...carries the implication that a larger volume header is categorically better than a smaller one. This is simply not true, as I already pointed out. One of the reasons Honda started using double walled pipe so long ago was because American buyers would refuse to accept the bike with headers on them that were the actual, optimal size for the engine.
if you want a lower volume header get a stock 07.
As far as the point at which one could consider the modified '08 muffler non-restrictive, I'd have to say that would be when both cones were removed, and the core was equal to the equivalent area of both exhaust valves, or 1.5" in this case. That's a bit arbitrary, and is dependent on several things that we haven't discussed. Nevertheless, with the removal of the rear cone, the muffler has certainly become less restrictive than it was, and one should be able to move toward a more nominal header size than the oversized '08 model.
Would I do it? Within my current budget, no, unless I could buy one used, and I might experiment with an '06 or '07 header first. If I had more disposable income, I probably would though, but not to get more power; to get more usable power over a wider range.