I too had the exact symptoms with my Giles pump.Mine would idle normally when cold and then basically stall when hot upon deceleration.All you need to do is adjust the screw for the throttle lever stop to bring the idle up,Or you could up the fueling too but if your smoking under full boost then upping the fuel is not a good idea.Its a very sensitive adjustment either way so It may take a coulpe days for you to get it where you want it to idle at.I'm not sure if your pump has the other idle adjustment working on the side as mine was disconnected for reasons only Giles knows,This is the reason you'll probably only have the option to adjust the idle by using the throttle lever stop.
With the amount of fuel that Giles has set our pumps to deliver it makes this adjustment very sensitive so with the test bench you can't qiute simulate the on engine idle.
If you are not going to raise boost any you may want to decrase the fueling to clean up the smoke under full load.Do you have an EGT gauge?