Since you are replacing everything, the fact that it was bose equipped means nothing (assuming your running new wiring). I would keep the tweeters in the dash or move them to the base of the a-pillars, keep the mids in the front and rear doors, shitcan whatever junk is installed in the rear deck but keep the grilles, and throw sub in trunk. Also, If your gonna do that much work invest in some second skin as well while you have everything apart.