Bondo Start. Since I fabricated my own top panel, I'll use Bondo to seal the edges, but inside the window cut-out edge, and on the outside edge of the case. More pics of this after it is painted
Final Cut-out. The case no longer needs the small metal lips to hold the PSU due to the flip. They're history...
Painting. I have to paint the case itself in two stages, one with the top and bottom masked off to apply the truck bed liner to the inside, and another with the inside masked to paint the top and bottom panels. Since I've added my own top panel, I can no longer remove the pop rivets to paint the panels separately. I painted each front panel component individually, since I've decided to go with a dual-color theme on the front: Flame Red (as was the original plan) plus Toreado for the front mesh and face drive face plates. Toreado is an interesting type burgundy, with red and purple highlights. It should contrast well with the flame red.
Also shown is the DVD burner's cover painted black to blend in with the inside, and the side panels, sanded down, and painted with self-etching primer (gray-green color), then wet-sanded before applying the color coats. This is only the beginning of the paint process.
CPU Cooler Mount Mod. The Scythe Ninja CPU cooler is really an oxymoron in and of itself. Only adults would spend the money on this cooler, yet it's package appears to be marketed to grade-school kids (ie: 10 year-olds). The name "Ninja" hints at Eastern history, and the brand itself is based in Japan, but the cooler's looks like a German cross when viewed from above. And finally, the cooler is top-notch for performance, but it's mounting bracket screams "lameness" since it matches the default Intel design with plastic clips, making reliable contact questionable.
To remedy this, I'm building my own mounting bracket, starting with its metal housing. Even though some people complain about CPU cooler mounts that need to have the motherboard removed, I love them due to their additional stability. So, I'm making my own. One neat piece of information I discovered: The Intel LGA775 socket mounting holes line-up
exactly with the mounting holes for an 80mm box fan. Sweetness. So, I rummaged through my spare parts and found a fan adapter, then painted it to match my front panel mesh (even though it will never be seen). To cushion this brace against the bottom of the motherboard, I used a freebie University of Phoenix mousepad. It's composed of rubber and cloth, so the pad is flexible and soft. I cut it to size easily with a blade.
The next step was to find compression-style springs that would apply constant pressure to promote better contact between the cooler and the CPU. Without springs, I would run the risk of either cracking the CPU/motherboard, or having a loose fit. Springs are essential for mounting brackets, and those without springs will have a semi-flexible metal bracket that acts like a spring. Since it's nearly impossible to find springs by themselves at a hardware store, I had to perform a creative search for them. Purely by a hunch, I found a decent selection of small springs sold as replacement parts for faucets. I bought a few different types to test them at home, and ended up selecting two of Danco's DL-4 packages (2 springs per pack) for Delta faucets. These springs provided an adequate amount of potential energy (resistance when compressed). In my bolt selection, I found the right sized bolts, nuts, and washers to hook it all up together. It appears to work very well, but I won't be able to test it until later.
Front Panel Mod. The front panel is going to get a major overhaul while keeping the original look. The most annoying aspect of the Matrix case is that it counteracts the ventilation advantage of its own mesh by putting far too much plastic behind it. To eliminate some of that, I cut out the excess plastic in front of the front 120mm fan, as shown in the first and second pics. Next was to make use of the Firewire/USB/Audio connector area. I never use Firewire for anything since USB 2.0 is almost as fast, and more commonly utilized, so I won't need its connection. I also never use the front audio ports since they're meant for a motherboard connector, and I'm using a separate sound card. Unfortunately, most sound cards are not friendly to front-panel connectors, mine included. So this leaves USB as the only connection I'd like to use.

And of course, since this case is flipped, the USB ports will be upside-down. That isn't too big of a problem, but I'm compulsive, so I'm using my own third-party USB header. To mount it, I'm cutting out part of its expansion slot bracket to mount over the existing USB cut-outs. I cut this bracket to size so that it covers the other holes. The only item left that I'd like on the front panel is a switch for the CCFLs. The Vantec Nexus fan controller comes with a switch, but it is fused with its own CCFL inverter (will only handle 2 CCFLs). Besides, I'd like the ability to control the 2 blue CCFLs independently from the 6 purple CCFLs. To mount a switch, I drilled a hole next to the USB headers. Since the panel is different now, I also had to sand down the raised symbols that designate each port. After modding that area, I used Bondo Spot and Glaze Putty to even out the surface (I forgot to take a pic of it sanded down, but I do have pics later of it painted).

Finally, I needed to do something about that gap in the bottom of the front panel. The bottom of the panel is now the top, so that gap for front fan ventilation is now an eye sore. The front fan has plenty of ventilation now with the cut-out, so it doesn't need additional ventilation. I could easily build this up with fiberglass, but mesh here would add some cool appeal if it appeared to blend into the panel itself. Also, this panel is almost exactly the width of the cut out for the top window, so keeping its shape visible with mesh seems like a winner. I measured plastic screening, cut to size, then sanded down the area to prep for the Bondo. I'm using the spot putty here since it works better with small areas.
Hard Drive Coolers/Silencers. I am impressed with the Nexus coolers I purchased, especially after comparing it to the Scythe SQD silencers. The Nexus one show here has mounted connections for SATA, IDE, and power, unlike the Scythe SQD silencer I've used in the past with other mods. I also love the easy install process. However, the cooling design really gets on my nerves. It only has two small strips of thermal padding to make contact with the drive. That is the only way this drive will cool inside what would otherwise become an oven for the drive. So, to help, I had to cut away part of the label for each drive (most likely voiding its warranty), in order for the strips to make contact with the drive, and not the label. The Western Digital Raptor drive will work without any additional modification, but the Western Digital RE drive has a breather port at the top. So, I had to cut away part of the thermal pad to make room for it. Otherwise, I really appreciate the aesthetics of the Nexus HDD silencer. I will have to monitor HDD temps closely when the mod is complete to make sure they live up to their claims.
Power Supply Mod. One of the few components that isn't new in this mod, even though it was used only for a few months, is the Enermax Liberty 500W PSU. It is certainly a capable and fairly stable PSU, but it's sleeving is pretty ugly. Black and gold are good colors on a PSU, but they really clash when put to use in sleeving. So, like all other cables in this mod, it will be sleeved with the same color sleeving. Did I mention that the highlights on the inside of the case are purple? Well, it should really contrast against the red and black case. So, a purple, acrylic PSU cover, and some purple sleeving should help. The stock gold fan grill might be a little overkill for a purple PSU cover (it looks almost like pimp colors), so I may change this out for a plain black or laser-cut chrome fan grill at a later date.