Results...

I now have the Stage One up and running on my '06 Road Star Midnight, and I love it. It's exactly what I was looking for... a little louder, and a lot deeper rumble. Just enough to drown out the 'sewing machine' sound up front.

I replaced my exhaust with a stock exhaust off an '05 Road Star Silverado that another fella had drilled. He went through the cones and then through the baffles. To me, it looks good... not perfect, but pretty good... and if you've got a steady drill hand, it seems to be less work and commotion than removing the cones. I've still got the old exhaust, and if I get anal, I might do a fussier drill job on that and swap it out again. But, to be realistic, I don't expect to spend a lot of time staring at the exhaust holes and worrying about how they look. Speaking of how they look, image file is attached (I hope).

Here's a little tech tip... there's a difference between the '05 and '06 exhaust. Being naturally lazy, when I swapped exhausts, I left my front pipes on and bolted on the other guy's mufflers to them. Bad idea... bad exhaust leak on the upper pipe where it meets the muffler. The '05 has a metal mesh bushing kind of thing on the male end of the pipe coming from the engine, which provides a good snug fit into the '05 muffler female. The '06 doesn't have that bushing, which makes for a sloppy fit. I assume the '06 upper muffler also has a tighter diameter, and if I'd tried to fit the '05 pipe into the '06 muffler (which I didn't), it would have been too big for the hole. I'm sure there's a connection between all of this and my love life when I was young, but I digress. Long story short, it looks like you shouldn't mix the '05 and '06 exhaust components. Of course, this is a scenario that rarely occurs.

Thanks for your help here, guys.