OMG! It hit me, just a minute ago!
Ok, on the panel covering the backside of the mobo, I'm going to attach three pieces of angle iron to the outside and use them to hold the acrylic. I'll use bondo to slope the angle iron in, making it part of the panel and the acrylic will be a window to the backside of the mobo. I'll use a CCFL on the bottom to light the water down low. It will be a part of the case and not a removeable side panel like I was originaly planning!
Now all I have to do is design the actual "tank" and I can get crackin!