First of all, you own one of the fastest PowerMacs of all time.  No, its not Mac Pro speed, but it did whip several models of G5s.  I think the big thing is whether you want to mod your case or use a new one.  I would go with a PC case.  Just that move will help a lot.  Its a tough mod for the inexperienced though.  The fans can and should be replaced.  I suggest Panalfo Ls.  Yes, there are quieter fans, but they dont move that much air.  You can set up a fan controller to run all of the fans.  The MB wont care.  I suggest the copper heatsink too.  http://www.smalldog.com.  It will take some money to get this Mac where you want it, but I have owned dual G5s too and still come back to the MDD as my main workstation.  The G5s made annoying beeping sounds, though the fans are much quieter.

One more thing...this models has a ton of expansion which keeps the G5s from coming back to my work area.  Okay, two more things, you could sell it and buy a Mac Pro or buy a MacBook pro.