The text became longer than I thought. Bear with me. I've also added a link for the pics in the previous post.
The project is now at point, where a lot of things that needs to be done on the case before I can even think of ordering the parts. I could order the parts in advance, but the money gets to me in early December, so I have some time to finish the case.
Let's talk about the parts before going into the case modding issue.
Two weeks ago I posted the latest parts list and some time after that I got mail from the taxman. It says that I'm getting about 1500e refund. It's half of the amount I expected, but hell of a bunch of money anyways. That money is the main funds I have for this project. I can ofcourse use a bit of my savings, but I'd rather not put too much of them in here. The budget means that I cannot go wild and get all the extreme stuff I talked about before. I have a rough outline of the parts I need and with all that, the money I'm going to spend is around 2k. I'll post the list later on. I just have to hope for a drastic price reductions :) We'll see what happens.
Then to the case modding. Last weekend I visited the farm again bout I was too busy fixing my car, so I couldn't do much for the case. However I spent some time placing the parts inside the frame and doing some sketches. I realised that I need to mount the stuff inside the case somehow. Not that I didn't know this before, but as I was trying different places for stuff I thought "how the hell is this going to stay there when this case is upright?". So back to the drawing board. This time I used good old pen and paper, so the drawings are a bit... impressionistic, should I say. I'm not going to put them up here, unless I get to draw them again with computer.
The final outcome of all this? The HDDs are going to be mounted vertically on a padded custom rack at the bottom, the alu tank and the pump also get their own pedestals. The PSU will be screwed on the ripped PSU plate welded on the frame.

Side view. Seeing this made me to rethink about my relationship with plexi and leds. Before I really did not like them too much and everybody is using them, but they should bring out the tank very well.
As for MoBo and optical drives I'm still thinking of the best solution. I think I'm going to fabricate a padded cradle for the optidrives and weld it on the frame too. The MoBo is a different thing. I'm still pondering whether the mounting plate should be fixed or removable. There are upsides and downsides for both ways.
If the plate is fixed, the design is easy and will not resonate much, but the assembly and upgrades are a bit tougher. Especially with the water cooling installed, I just can't flip the case on the side to get my hands on the parts.
If the plate is removable all the stuff I need to do on the MoBo becomes very easy but I need to find a way to make the design simple and resonation free. Some padding here and there kills the resonation, but the design still awaits for my discovery.

Front view. This setup looks pretty OK to me.
I'm also going to scrap the radiators I bought earlier on and buy a factory made one. The Ibiza rad is aluminium and the other is copper. That copper rad might be too small to handle all the heat so I'm getting one large one. The fans I had from my dad's stash are fixed on a frame. I just need to put in some guides for air because the fan frame is not as big as the overall frame. Mounting the radiator on the fan frame should be piece of cake. I'm still thinking of getting some ordinary 120mm 12V case fans instead of those industrial grade 120mm 230V fans mounted in there.
Since the shit hit the fan with alu/copper corrosion and I decided not to use my tank, I've got another idea. It would be terrible waste to throw the tank away, so I decided to get a pastic tank and fit it inside the alu tank. Then I'm mounting the tank inside the case and putting some plexi and a led to show it off.
Plexi and leds were not considered to be used in this project initially in my plans. The initial plan was to cover the entire frame with thick rubber plates and mount the alu tank outside. After trying the tank inside the case, I thought it'd make a nice flavor to it. Also the rubber plates I planned to use look so worn out that the case would look like crap. Therefore I'm going with that neoprene stuff pictured earlier. It doesn't look so porn as black rubber, but what can you do? The good thing is that I can replace the cover plates later, if I get my hands on some good porny rubber ;)
At this point I'm thinking if I bit more than I can chew. I'm not worried about the parts or budget but the case. So much work and after finishing one part I find out that I need to do two more that I wasn't even aware of to make things work. Well... such is life.