OK, I've finally got around to uploading some pics of the case, but I'm almost off to work, so I'll only make a start. Here's a quick guide on how I cut the top of my case:
Tools (didn't take a pic sorry):
-Masking tape ($4 for good stuff)
-Set square and pencil ($7 at Bunnings)
-Jigsaw, Dremel, or both (with a metal cutting blade) (prices vary. $50 for a cheap dremel, $70 for a cheap jigsaw)
-Drill and a couple drill bits ($50 for a cheapie)
-400 and 800 grit sandpaper ($3 for a sheet of each)
-Cup, plate, protractor, CD (anything with a round edge)
-Bastard File (with a rounded and flat edge) ($15 - $20 for a nice one)
-A set of clamps ($12 at Bunnings)
The first rule of cutting anything is to measure twice, and cut once. The 240mm rad was an absolute terror to measure, due to the design of the metal brackets that the fans bolted to. They weren't at all symmetrical, which meant a lot of measuring and re-measuring before I got it right. In the end, I just circled the fan holes, and made my own cutting template from a set of consistent measurements (and my trusty cup). Here's a few pics of the measuring and cutting process:

I left some play with the corners in order to allow for me to have some control with the file and sandpaper. The final image on the right is after the holes have also been de-burred using a pointy dremel grinding bit. A week later I added another hole for the rear of the case, in an effort to discard the side fan, and just use a single top mounted exhaust one. I followed the same dimensions as the previous holes. Here was the final result:
The next step was to slightly modify the motherboard tray so I would be able to route my cables behind the tray out of sight. Being very pedantic with cable management (I hate them), I wanted to make the fitting and hiding as easy as possible. I'll upload the photos soon of what i've done.
Onto the motherboard tray cutting. I mounted the mobo and measured about 1cm from the SATA ports and also the 24 pin ATX lead. Then, I found a 1/2" drill bit a put 4 holes at the top and bottom of each cut. Then it was as easy as grabbing the jigsaw and bridging the gap, filing and sanding. The ATX cut needed a slight semi circle file to allow for the clip to fit. The other cut near the mobo tray was an extension to the top standard hole (on the tray) and a rear cut on the supporting arch for the ATX, SATA and PSU cables to sit in without obstructing the closed side panel. I didn't take a photo of the final cut though, maybe later.
Next up, the mounting of the front 120mm rad. It was a little larger than expected, which mean some more dremelling work at the front. The side shroud stuck out higher than the aluminium sheet for the drive bays above. The cut was a VERY snug fit, which is good cause it actually hold the rad in place a little really well.
