Since I've been there and done that, here's a tip:
The ECU need to "see" both the existence of the secondary throttle motor and the relative position of the secondary plates (via secondary TPS). So you will get a constant "check engine" light unless you keep the secondary motor connected to the secondary TPS by a short piece of rod (and maybe store the removed units under the tank). IMO, not worth the bother... I live with the light.
Remember: You can't read tech tips like this on R3Owners.com 'cause they ain't been there!