Might try a different scanner, to see if it is lying to you. The other thing that could be causing a desired idle of 1000 would be what they call the throttle cracker, and throttle follower that basically act as the old dash pot that slowed the transition idle. Was this a manual transmission been to start with or is it converted from a automatic transmission? The automatic transmission bin has several rolling idle settings that affect idle while the vehicle is in motion.

Did you ever try plugging the hole for the IAC that I suggested much earlier?