Yeah, you could rig something with the orignal throttle switch as you say, I think they have an idle switch as well as WOT don't they ? a 1k pull-up from the 5v rail to the idle switch pin (with the common of the switch to earth) would suffice so that you had 0v at idle and 5v when there is throttle movement. you could play with the adc settings in Wari to show the 5v as 50% throttle, or whatever number works best I found the GTA's engine doesn't need much (if any!) pump after 1500rpm so an idle switch arranged as above would work well enough to get rid of the stutter comming off idle.
Re closed-loop, I havn't ever used it so I couldn't comment sorry. I'm a bit old-skool when it comes to tuning, I don't trust much, least of all software. I hear it works well for some people. Have you had a snoop around the
www.adaptronic.com.au forum ? I think the problem you describe has been discussed before, worth a search. Maybe it's a firmware glitch, I'm guessing your using the latest ? so far for me it has been pretty glitch free.