Bill,
Oh boy, have you opened a can of worms! I will share the very short version of my opinion with you. If you want to tinker with air intake -> exhaust you really need a way of measuring the effect of what you do. Too much air through the system and things lean out very rapidly, causing all kinds of "rideability" issues, deceleration popping/backfiring, and potential damage to the engine. On the other side, too much fuel in the system and you get incomplete combustion AND (this is what often gets overlooked) overheating of the engine and gas in the oil (which quickly ruins your main bearings).
I have always used a fuel/air monitor when tuning engines of the modern era. Just before I bought my Valkyrie I bought an Innovate LM-2 to tune my Moto Guzzi (
http://www.innovatemotorsports.com/products/lm1.php). These systems are often used by race crews to "tweak" air/fuel mixtures to match weather and track conditions, etc. It is in perfect condition (about ten hours of use). I'd be glad to sell it if you decide you want to do some serious tuning.
On Moto Guzzis the O2 Sensor is active in the lower RPM range. It is not part of the MAP at "cruising" speeds (appx. 3000 RPM and up). I think I'm remembering that right - lots of water under the bridge.
But back to your question. "Closed loop" systems (ECU adjusts Air/Fuel Mixture based on O2 Sensor input) can handle some increase of air input, but not too much. They can also manage a change in the exhaust, if the back pressure from the exhaust is not altered significantly. But, when you change either a great deal, or when you change both, you are liable to overwhelm the Air/Fuel "MAP" in the ECU - it just doesn't accommodate the dramatic change. Then you have to "re-MAP" your ECU or run the potential of damaging engine parts. HD riders are notorious for doing such things and then wonder why their scooters run so poorly.
If your scrambler has carburetors you're in luck. They can be easily re-jetted to accommodate the changed air intake/exhaust. If it has an ECU then you are likely to need a re-MAP.
Hope this helps a bit. If you pursue things be sure to get an air/fuel meter of some sort so you can tell what is really going on.
Good luck!
Bill