What PC are you using on the APL? That's where I would put the effort first, if you've not already done so. With the amps, I've had excellent results with the Z-Squared Elite I cables, which can be had on auction or used for around $250 each. I'm using them on a pair of 50W triode monoblocks, and after a week of break-in, they sound open and relaxed. I've tried maybe 4 or 5 other PC's, up to the $800 price range, and I find the Z-Squared to be the most 'absent' (read: transparent) of the bunch.
You might also try putting the Zu PC's on the amps and running them direct to the wall. I have found our SET amps to generally sound constricted by conditioners. It may be worth a try, just to see what you think.
Best of luck. That's a very nice system you have, by the way.