Back-to-back questions are no problem at all.  Especially when they
are good ones :)

I've integrated many things similar to Mobiscroll (such as iScroll,
CanVG, etc) using the iUI 0.4 extension mechanism.  You can take a
look at some of the example extensions in the iUI 0.4 download.  (If
you're adventurous try the latest CI build which has an improvement to
the extension events that makes things a little simpler.)

There is also the Countdown App (http://www.technetra.com/2009/08/10/
countdown-iphone-webapp/) from iPhoneDevCamp 3 that integrates
SpinningWheel (http://cubiq.org/spinning-wheel-on-webkit-for-iphone-
ipod-touch)  It's from 2009, though and it doesn't seem to work well
on recent iOS. I just tested it on iOS 4.2.1 and it works great.  (I
don't think SpinningWheel ever worked in desktop browsers.)  Note that
the SpinningWheel integration was done with iUI 0.3 which didn't even
provide the events/extension mechanism.

If you could post a sample app that integrates the two, we can look at
it with our browsers/debuggers.  (http://jsfiddle.net is one way of
doing that)

The first thing I would look at is the CSS to make sure there are no
conflicts there.

Regards,