After about 3 months of setting my car up on the factory ecu I was finally satisfied I could not make it run any better and that it was time to install the PFC.Using the Apex manual and Dale Clark's PowerFC FAQ,I pulled the 4 wires by releasing the pins from the connector blocks and taped them up,located the PFC and fired her up.All 3 idles set perfectly,AC works with all 4 fan speeds,3krpm hesitation gone and engine is just smoother all around.The only downside I have noticed so far is the secondary turbo transition--it is just not as smooth as with the factory ecu.

So thanks to all those who have posted good info and saved me lots of experimenting.So next phase is to run a while like this,play around with the Commander and then progress to a datalogit.

My modification list includes fully sequential BNR turbos,JDM downpipe,RB dual tip,a version of the Cheap Bastard cold air intake,SupraTT fuel pump,Greddy E-01 Boost controller,ACT Pro-lite flywheel,Exedy stage 1 clutch kit.

 

The PFC lets you adjust boost for before and after turbo transistion.
Read the manual section about boost control very carefully to avoid fuel cut.
Maybe this is the problem. If not, then with a Datalogit you can actually change the point of transistion which some have done by having the secondary turbo come active sooner by about 500 rpm.