is there any to hook up a aftermarket stereo
 

with factory bose amps without useing a bunch of adapters

Yes, I used a bypass wiring harness. Don't buy from crutchfield's the harness is ok but the instructions tell you the wrong location for installing it. After hours trying to figure it out (and talking one of their "experts") I checked their forum & found a post from almost 2 yrs. prior from someone who got the same instructions. I was PI$$ED! They ended up telling me to keep the harness & refunded my $. Then had the odasity to email informing me of the refund & telling me basiclly to shop somewhere else because I odviously needed more service than they could provide. Yeah, correct instructions for installing a product they sell!!! And I still get their SPAM sale ads.
You will need 2 run new wiring for the speakers as well.
Good luck, hope this helps