I just installed a 940bt and relocated the mute wire and grounded it and the parking wire.  As of right now the auto eq button is greyed out.  

I ordered the pioneer autoeq microphone and wanted to know if theres going to be any issues using it while bypasses.

The microphone should be here today, i'll update whether or not it works with the bypass

I have my 940 bypassed and I have nos issues. It works fine.

Thanks!

I just tested it out and it does infact work with the bypass (relocating mute wire)

Tricky thing was, was that if you just hit the "eq" button on the AV screen, the Auto Eq function is grayed out.  If you go (with the mic plugged in and the source set to Off): Home, Settings, AV Settings, Auto Eq, and hit start....it works like a champ!

Where do you actually plug the mic into to perform the Auto Eq test?

It plugs into the 3.5mm socket on the USB cable (iphone lead).