The 088 ATS turbo sits pretty much directly on top of the controller. When I had my 088 I was always waiting for the controller to crap out and have to remove the turbo to change it.
With the newer wastegated turbos, you can remove the airbox assy. and still get to the controller without removing anything else. I've serviced mine (replaced the harness) since installing my Aurora 2000 kit.
If you can ID your turbo as a non-wastegated ATS unit, you will likely have to remove it to gain access to the controller. Another option is to disconnect the batteries, remove all the wiring from the studs of the controller if you can get a wrench on the nuts on the studs, and install a new controller on the valve cover, abandoning the stock controller under the turbo.
Good luck!
Ryan