Mark,
I am having the same problem with engine/alternator noise only with the H3 phone or onstart is active. I have the exact same setup that you have except that I am not using the OS2-Bose adapter. I'm using just the OS2 non Bose adapter. If they find out what the problem is, please let me know, and I will do the same.
Regarding the nav shutting off, that is a install problem. They must have the mute wire from the OS2 hooked up the the system remote on the AVIC-D1 or something like that. This feature works fine on my system. Make sure they have the Mute wire from the OS2 hooked up to the Mute wire on the AVIC-D1 harness.
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