I see, i was thinking of something slightly different when i posted my suggestions. Hmm, i have to say (and this i just a personell opinion) i think it will always look a mess with cable all over the shop. I do like to first image you posted with the perspex box. I think that you should think about coming half way, set up a sort of perspex tray/shelf suspend in the middle of the tank on which to attach the mobo and bit and bobs. You are really going to have to be tidy with the cables. Maybe cut a few holes in the tray and run the cables for the hdd, power, swtiches, etc under the tray hence under the mobo. Then wrap it in you clear perspex / whatever
You really need to think about how your going to cool the cpu, you are certainly going to need water cooled, florinert seems out. If you vacumm form it that may work, i dont think the forces will distroy the onboard components as long as it done slowly and the vacumm forms equally around each component. But i think you will stuggly to get one that look very clear. You going to need a large gromit for all your cables the enter the tank.
Personally i would make a small clear sealed perspex box, and put the bits in, add one gromit hole for all the cables and cooling pipes. This would be very easy to do. Once you have the water in the tank i dont think you will notice the perspex any more or less tha you would a vacumm formed "skin" around the board. You could suspend the clear box at an angle in the middle of the tank, put some bright leds in it, bit of gravel on top, and a small water plant. maybe even a little castle for the fish. You will need an air pump to oxygenate the water for the fish, you could put this under the clear perspex box and the bubbles would raise and hit the bottom of the box and then spread round it which would look cool, kind of like you board was fizzing.
Also i just thought!, you should take a normal pc case (one that looks cool and is quite big).then mount all your components on the case pretty much as normal. Replace the side of your pc with a clear perspex, of even a high % lead glass (which may be too expensive). Then seal the case completely (which would be easy), you could put the box straight in the water and then place the original side (which you replaced with clear perspex) at a random angle from the box, the effect will look like you have dropped the whole case in the tank and side had fallen off but yet it still works!! That would look loads cooler. It will look like a computer dropped in a fish tank rather than a bunch of PCBs scattered in a mess in a fish tank. You could combine ideas, eg vacumm forming the mobo, and still mounting it in the case (this way you dont have to seal the case).