I just completed the swap today. It was very easy.
On the hardware side (besides removing the old board, etc.), I had to clip the cable retention tie wraps because the USB headers and firewire header are located far enough away on the new board (EVGA 780i SLI FTW) to make the cables not quite long enough. I also had to reroute the cable for firewire going to the front panel under the fan (an air gap is available) because it still wasn't long enough. No big deal though. Luckily (or by design) the cable for the front panel LEDs is exactly the same as the Dell board. Likewise, the audio header for the front panel connectors is exactly the same as the Dell board. Very much good! It really felt like the two boards were designed by the same shop or there are motherboard header pin standards I'm not aware of.
The bigger issue is the CPU cooler mount (four screws). There is a "screw width" difference between the two boards. The problem is the "plate" the cooler screws into is connected to the chassis; not the back of the old motherboard. I therefore had to unscrew the plate from the chassis, and then mount it directly to the back of the new motherboard and then screw in the old CPU cooler. I left the plate unconnected to the chassis as this really is just more mounting points for the motherboard to the chassis. Aren't 10 screws enough? The chassis-attached "pads" previously under the plate are still making contact with it even in its new "mounted-to-motherboard" orientation.
I was very careful to plug the drives into the same SATA ports on the new board. The board has SATA0 and SATA1 mounted "edgeways" instead of "up" like every other motherboard I've seen. SATA2-SATA5 normally have up-oriented mounts. EVGA ships SATA cables that have locking clips to help keep the cables connected. I hadn't seen this before, and it seems like a good idea. The only slight problem was that they are straight connectors as opposed to the Dell connectors (right angle). This isn't an issue on the motherboard end, but it does cause the cable to stand up when connected to the drives.
After that, I powered the board up, verified the hardware it found, checked out the BIOS settings (I changed it to full logo display), then booted into the Ubuntu 64-bit (8.04) half of the machine (dual-boot). It came up fine and seemed to run faster. I then restarted and went into XP x64 (really server 2003-based) and it came up with a low resolution screen and the keyboard and mouse didn't work. Yikes! I let the disk spin until the LEDs went out (reflecting startup and reconfiguration activity), then I reconnected the USB connections and everything was recognized! I then logged in. Windows gave me a message saying new devices had been added and needed to restart. I did and everything came up fine (at normal resolution too!). The drive labels were just as they were before! The sound even worked, which I didn't expect. The only odd thing I noted was that the network connections had new numerical suffixes (#2) for the firewire network connection and the network links (#3 and #4). I renamed these. The Windows half seems just fine. It didn't even ask to re-activate. My windows install is off an MSDN key, so maybe that had something to do with it. Anyways, everything worked, and it seems to be faster. I verified with the tools you mentioned that the PCIe slots are the full 16 lanes, so all is well.
Dell should have just used this board in the first place. Besides the correct PCIe lane allocation, I now have an additional x16 slot which I could use to build a 3-way SLI box. I now also have an extra gigE port, two extra USB ports, and an optical audio port on the back. If I wanted to, I could also install the connection for a serial port.