The "in gear" switch is on the shift plate if it has one.

I don't see any wiring or harness for a gear position sensor. I started engine and scanned again today. I raised TPS voltage to .65 per Whipple. No change, still idles warm about 980. If I bring the TPS voltage down to .10 it lowers the idle, a little from 980. I also increased the IAC % with the scan tool, I could hear more air at the IAC but no real change in idle speed. I held the Whipple throttle plates closed and that did not lower the idle either. Injector test was fine. I took the throttle linkage off. If I start the engine, rev it by hand, the idle goes up and rests at 1280 and will not go back down. Putting pressure on the linkage does nothing and the Whipple idle screw is not keeping the idle high. I took the IAC filter off and plugged the intake while it was idling. It lowered the idle some, but as low as 750. It did seem like it was running a little rough and on the edge of stalling. When I plugged the IAC intake, the scanner read IAC duty 99%, when released, IAC settled down to 10. I have looked over the vac lines and the Whipple again, I don't see or hear anything unusual.

Plugged the IAC and it still runs and throttle plate is closed. IMO you have a vacuum leak.

Use WD40 and start spraying or propane (unlit) and move it around to see if anything changes the idle