Read this
http://www.max-boost.co.uk/max-boost/supra/boosting_the_beast.htm
It sounds to me like he has fitted the controller to the ebv at the back of the engine, which does NOTHING to up the boost of turbo 2.
This will only work with control of the wastegate valve, which seems he hasn't done.
Follow Scotts advice, the link above shows you how to plumb it back to stock.
The Max Boost site tells you to fit a MANUAL boost controller to the EBV, where your current control is, and a manual/electronic to to wastgate valve, thereby controlling the presooling and boost of No2.