I have a 94 740i and I want to upgrade the headunit, does anyone know if you can upgrade the headunit and run it thru the stock amp, if so are there any special adapters I will have to use or is it a straigh RCA conection, or will I have to change out the amp as well?

I put an Alpine unit in my 1988 750 and bypassed the factory amp. Today's internal amps are generally much better that the older factory, OEM ones so that is why I used the head unit amp, and it works great.

Thanks for the info, one more question if I may,

all the speaker wires right now would be running to the amp, correct? So I would need to reroute or run new wires from the head unit to the speakers?

YES. The Alpine unit I bought had 5WX4 power and it sounds great, Fader, Balance,Bass.Treble,Equalizer and CD player, and except for the wiring, it was a plug and play operation.