Jason,
I¡¯ve got an ¡®05 ej25 in my Vanagon that had the very same issue- drove me nuts. It would stall every time I came to a stop. The solution to my issue was allowing the engine to warm up and idle for 10 minutes before driving. I¡¯m not sure if it¡¯s related to the ECU, but every time I¡¯ve let it idle for 10-15 minutes, it¡¯s not stalled since. Maybe others can chime in as to why. My engine code was P1492, EGR signal. The stalling didn¡¯t matter if the EGR wiring harness was plugged in or not. ?
Greg