I decided the easiest way for me to bypass the bose system is to get rid of it all together. I was planning on installing the new pioneer d3 with a 4 channel amp that is 2 ohm stable to run the stock bose speakers(rated at 2 ohms). In doing so...will taking out the bose amp affect any components in the car? Im asking because one of my friends who install a tv had to keep his factory headunit plugged in the trunk to keep his car functioning properly.

Thanks any input would be appreciated

the only thing you will loose is the radio display in the instrument cluster.