Did you use the RCA outs.
How does the metra harness run the Inputs to the Hi Fi amp?
The Hi Fi amp is only meant to accept 5 volt differential signals.
If this thing hooks it up as common ground single ended Inputs it won't work. You will need a adaptor that converts to differential inputs.
Do you have pinouts of the metra harness and the OEM system.
When you say he checked it out do you mean measured with a meter.
http://www.e90post.com/forums/showthread.php?t=641323
The harness may assume the base system is
what you are working with not Hi Fi.