Hi,
OK this all may seem obvious, but we could do with a bit more info, if we are to help.For example, it may help Alex better identify any significant issues if you can elaborate on what you mean by 'deep profiling'.
With audio, are you using compressed audio?, are you decompressing on load, what type of audio is it, mono, stereo, 3D?
You are not instantiating any objects at the time of the stuttering are you? Have you checked how much memory you are using on the lower devices? Any memory warnings in xCode? Did you optimise all your textures? What size are your textures? Do you have mip mapping turned on? how many textures are you using? How many materials are there? What draw count are you up to? Which version of Unity are you using 1.7? 3.x? iPhone normal/Pro?
A quick question, how come you got to the end of you project before you noticed the stuttering, this is not intended to be rude, just wondering if something you did or added towards the end has inadvertently affected the project adversely?
How many objects are you talking about? particle effects? how many sounds are you trying to play? Do they have any effects or filters on them?
That should give us something to optimise, maybe!
IPete2.