sorry I've been out of the loop for a while, I ordered parts today to build a logic analyzer so that I can compare what my (working) usb obd reader does compared to my arduino and adjust accordingly (only like $10 in parts). I'm also thinking I'm going to have to ditch the pulseIn method and setup the analog comparator manually
off topic, the logic analyzer should also come in handy in getting my arduino to control my zune, which is the only thing I'm lacking with my integration setup compared to when I was using an ipod, woot!