Good to hear you're running the right ECU.
When your shop told you that a new ECU was needed, how did they retrieve the ECU fault code? Since a missing VTEC solenoid signal will send the P72 into limp mode, I highly doubt you need a new ECU.
RE: WIRING
As for the VTEC wiring, a competent shop should have:
a) known they were dealing with an LS and
b) run the additional wiring already.
Here's a link to a related swap with the pinout for a P72 ECU.
http://hondaswap.com/hybrid-ed-ef-da...ut-help-83614/
If you paid your installers to handle the wiring aspect of this swap, then the easiest solution is to let them do what you hired them to.
RE: FAST IDLE:
Since you detached the cable and there's no doubt that the throttle is closed, start by checking for vacuum leaks.
A footnote: As I said earlier, make sure you're using a GSR throttle cable and that there is no slack in the throttle cable when the throttle plate is closed and the accelerator pedal is at the top of its travel.