Yea, I never noticed a difference. Your not going to add 20whp by doing anything drastic. You gotta remember that there is "play" in the bolts when tightening it down too. So the pieces can shift and your work could end up for nothing. Using dowels is the only way to insure a perfect fit and seamless flow. I'd guess 1-5whp gain in the process? I didn't spend a lot of time on mine and it works just fine.
Just look at head castings. You'll never find a head with "good" runners. The losses will add up, but it's not a huge difference. I'm pretty anal, and seeing it bothered me, but my rational side took over and I didn't bother spending hours of grinding and sanding to make that few extra ponies. I did look into some sort of a flexible sanding tool that would "snake" it's way in the runners to smooth them out and add a some CFM of airflow, but I came up empty handed. Best thing to do would be to have the whole manifold extrude honed, but that could cost up to $400. I think cutting the plenum off and welding on a bigger one would yield much better results in the high end. I think it was Garfeild Wright that did that on a few Cyclone manifolds and had good results.
I'd rather just add 1-3 lbs of boost.... but to each his own.