Javascript performance on mobile Safari (iPad) is much more sensitive for my application that it is on the desktop. Some operations that work super-smooth on the desktop tak
You could try using a javascript profiling library (using timers for example) by a bit of searching I've found http://remysharp.com/2007/04/20/performance-profiling-javascript/ but since I didn't test it I can't tell you if its any good. You could place timers at various locations in your code and try to track down the bottlenecks that way.
(Js Microtime Library http://phpjs.org/functions/microtime:472)