99 audi with bose pinout

I recently purchased the American International Harness #< face=Verdana color=#222222 >VWH-1004 and antenna adaptor for this 99 Audi A4 w/Factory Bose.  It consists of two harnesses, one with a power plug and a speaker out and the second is additional speaker out intended for the premium sound package.

My problem is my radio contains a fourth plug which contains the line level out to the rear amp.  The only plug that will actually match the pinout on a sticker above the radio is the power plug. When I trace the wires through the plug most of the wires connect to a blank pin from the factory harness, and vice-versa.

I have looked through the catalogs of Metra, American International (the one I have now), and scosche with no luck in finding a fourth plug.  Will I have to cut the plug? Does anybody make and integration or bypass harness for this type of car?

Anyone familiar with these Bose systems?

From what I understand the amp is the one next to the changer in the trunk.  Does anybody know the pinout for the amp?  Worst come to worst I can replace it with my own 4-channel and replace the interior speakers, but we would prefer to keep the factory Bose inside. 

At the end, it should end up a Pioneer headunit with factory Bose interiors, and an additional amp for a pair of subs.

Thanks in advance for anyone who can help shed some light- FrydChkn

"it is what it is, and to each their own"

Try this.

https://www.the12volt.com/installbay/forum_posts.asp?tid=78249&KW=audi+a4

[  Is there a small yellow plug behind the radio?  if there is, all the wires you need as far as the audio and remote turn on lead will be there.  What you need to do is get a cheap set of rcas and cut the ends off about 4 -6 inches back so you have some wire to work with.  If you look at the top of the radio it'll give you the pinout of that yellow plug.  From there cut that plug off, just make sure you leave enough wire on it so if you need to you can reattach it.  Then take the rca ends and solder the center pins to each of the positives lf,rf,lr,and rr.  Take the ground sheilds of each of the rcas and solder them to the ground in that harness.  There is one wire left in there that will be the amp turnon. Hook that up to your new radio, then tie power in on the vw harness as normal cap off the unused wires and you should be all set.  Need anymore help let me know, have done this many times without fail.  ]

Thanks for the info cntrylvr79, I was pretty much headed in that direction until I read your post and it kind of threw me off a bit.  I don't have a small yellow plug, but what I do have is an orangish plug that is supposed to be the speaker out plug, and it has a (+/-) for the front left speaker (I already read your post for what that is for). Now, I do have another black plug that doesn't match any of the plugs from the installation harness.  It is a 20 pin black plug that contains what seems to be the changer controls, remote, and line level inputs for the factory amp. 

Could it be that its not yellow and has that large black plug instead because this one has a changer?