ullr

I figured out my issue, the AT/MT identification wire was ungrounded. This article was a fantastic resource. http://www.shoptalkforums.com/viewtopic.php?f=19&t=145631&hilit=neutral+switch

I too am having this same issue with an EJ22 that I swapped into a vw bus. Do you recommend changing out the IAC valve or adjusting it? Or is this just something to live with? There must be a way to get the ecu to recognize it as a manual transmission.