I have the exact same settup as you.
My pump doesn't really create a whirlpool... more likie a spiral hot tub of wort goodness. I use it for re-circ., transfering, cooling, etc., but NOT for whirlpooling.
Here's what I do, and works well...
Use the pump to aid in cooling. Once you get it down to pitchable temp, pull the IC and use your (sanitized) spoon to give it the whirlpool. Stir it as fast as you can, and then cover it for no less than 20 minutes. An hour is better.
Siphon/drain off the wort, and as you get towards the bottom you'll see the trub. Drain off as much as you can without sucking up the trub.
Keg #1: Bourbon/Oak Vanilla Porter
Keg #2: Cascadian Stout
Keg #3: BMC West
Bottled: Mjolnir Mead, Lazy Daze Hefe, The Bollocks ESB, Dark Matter stout.