The difficult part of this is that OTO/EBA stores songs as fragments, and pieces them together to avoid redundancy. Therefore, something like the chorus would only be stored once, and it would know to play that fragment at 0:37, 1:41, etc. AFAIK no one has figured out how it actually does this or where to change it.

 

@kesadisn:
I am aware that they were all cover songs, as I stated in my original post. Also, I don't think they are cut, as when I am listening, my (musically untrained) ears cannot discern any difference that will cause it to be 100% off-beat.
@chuckstudios:
Is it possible to just cut the original in the same manner and replace the fragments with other fragments?

 

@mishydishy:
try to hear Pop Star song on Ouendan 2 and hear it on full song
you'll see the differences
need more?
Hear Shonen Heart too
or COUNTDOWN

i'm sure you'll understand