The problems with the bose systems skipping comes from the head unit and it appears this has been removed and replaced by the Alpine double din.
As for the cd changer this is integral to the bose headunit as you just feed the cd's into it and as i mentioned earlier appears to be replaced with the alpine double din.
With an install like this its hard to work out what Bose stereo is left as if the bose amp is being used it would be to power the standard component speakers and i would have thought that these would have been upgraded with the money that has been spent on the subs, amp and headunit.
Hope this helps