Sorry for a delayed response. Real life issues always take precedence.
Ace: Yes, the VM series do have odd numbered Needle Jets. I had considered going from a Q6 to a Q5 until you advised the P6. Glad I took your advice!
creaky: Close is kinda like hand grenades when you compare an IB 500 with stock exhaust to an AVL 500 with free flowing. I think the stock 2006 IB has the coated header with a 2-stage Cat in the silencer, correct? Or maybe it was only the case with the AVL. Dunno.
I could only make suggestions in this case, but this worked for me, so if anyone else feels like correcting or confirming anything I say please, please,
please feel free to do so. I will not be offended since this has been (and will continue to be) a learning process for me, too.
This helped me a lot, as it gave me a map to follow. You may already have this, but maybe someone else can use it, too:
http://www.mikuni.com/pdf/vmmanual.pdf I highly recommend downloading and printing it.
Page 14 is a good Troubleshooting section to determine Lean or Rich performance conditions.
The last page shows the throttle settings on the left and which Needles/Jets come into play at the various throttle settings on the right.
I don't know what assumptions Mikuni makes regarding breathing on the Main Jet Tuning Calculator but it worked for me with the Goldstar system. I ordered up a Main Jet Kit (4/042 series with #70-#230 main jets) from jetsrus.com and it came with a calculator, but the calculator alone is also available cheap all over e-bay.
Ensure your Air Filter is CLEAN! Accumulated dirt or over-oiling will definitely degrade performance. This is even more important with restricted breathing such as with a stock exhaust. If your filter is dirty or over-oiled and you start messing with your jetting, changing to a clean filter later could just give you a leaner condition and may require re-jetting.
Ensure there are no air leaks on the intake side. Any crack or bad seal will automatically make for a lean condition and reduce performance.
You say it "runs OK now, but could go better". Is acceleration poor across settings? Maybe go richer on the Jet Needle a slot? Mines set at #3 position (middle) and runs well. Any slot adjustment (Fuel Ratio) IMHO is the very last step you'd need to do, especially if performance suffers at all settings.
Do plug chops for each throttle setting. At idle with no load, and at all settings under load. That will tell you more than an O2 gage whether you need to go leaner or richer with that particular needle or jet. A gage can be out of calibration and give an erroneous indication. Plug Chops don't lie.
As for a silencer recommendation, I'm using a Short Reverse Megaphone on the UCE and a Goldstar System on the AVL. The Goldstar system doesn't strike me as particularly loud compared to the Reverse Meg.