Is the ub400 dongle good or not? The author seems to think so, but your responses seem to contradict that and then you say he fixed some things and it's working but it is a little unclear if you are referring to your built-in dongle or the suggested one that eventually works without issue.
After some testing, my conclusion is that the built-in BT in my particular system didn't cause the software to behave any differently than the CSR 4.0 dongles I already had, or the UB400 (same CSR 4.0 tech) I purchased later. But how well the internal BT works may vary across systems, as there are multiple different chipsets and the tech could be old and not fully compatible. I tried an old laptop, and while the software worked, the updates were so slow it would be unusable.
Fusselkroete is currently looking at certain aspects of the software to see why it breaks on one of my systems. He has already sent me a test version which disabled some things and it worked 100% better on that system, so he knows what's causing it and is now trying to figure out why. On my 37" CRT with a quad-core, the normal release version works fine.
At least in my case, a $5 CSR 4.0 BT dongle works, so there's little reason not to get one. Many probably already have one laying around nowadays. But the software is free and available, so I recommend just testing the built-in BT and only try buying a dongle if the software isn't working correctly.
Anything concrete on the wide angle lenses?
Not at this point. I bought one like you described, but I have no idea how much they vary across vendors, or whether it's even optimal for this. One thing I can just about guarantee is that it will not perform as well as it could, if strapped to the front of a controller. The distance between the camera and first lens should be as small as possible to prevent vignetting of the final image. Focus could be affected as well, but that's probably not the biggest concern with this type of camera. Oh, and center alignment is SUPER important. While the camera MAY be in the exact center of that little window, it doesn't need to be to perform correctly as it's designed. If it isn't, and this is what the mount is based upon, then it won't be correct so that stuff needs to be verified.
While not certain, I do believe that Fusselkroete will eventually need to add lens compensation to the 4-point tracking in order to make it perfect. With a cheap "fish-eye" lens, the image will elongate at greater levels the further from center it is. This would have implications for accuracy, so should be accounted for.
Without one, at least with a 4:3 monitor, I don't find myself needing to stand further back than I would normally with an actual lightgun. Then again, I'm not a "screen basher" when I play.

In regards to the leds themselves I think I can design something to clip them into that wouldn't add to their footprint. Perhaps a disc with some lines printed on it to aid in alignment.
You certainly can, but it would really only be for cosmetics. Some good, strong double-sticky on the back would be good for mounting as well, with the larger surface area. Personally, I wasn't concerned with that, as both monitors have dark bezels and are in very poorly lit environments. The black, cloth gaffers tape I found a long time ago at the dollar store worked perfectly. (I really wish I bought a case of the stuff...makes duct tape look like the junk that it is.)
It looks like you seem to think a standard 6.5v power supply is good for the leds but if we can get a system down to 3.3v 300ma (unlikely I know) then it could just be plugged into the usb port in the back of most modern flat screens and make the setup far less complicated, especially for non-permanent setups.
Unfortunately, it's not possible without giving up a lot. The Wii could get away with cheap, low output LEDs because there were only two LEDs (well, clusters, but they were at different angles) and they were positioned a lot closer together. That means you could be a lot closer to them so the output could be lower. That said, the Lichtknarre software allows the use of a Wii bar with the correct plug-in, so you may be able to go that route if you are willing to sacrifice accuracy. But I had no interest in doing that. If you want the best results, it takes a bit more effort.
And more importantly, if you go with the 6.5v supply, make sure it's a GOOD one (i.e. well-regulated at that voltage and with more than enough current delivery) AND you use an appropriate resistor AND the wire gauge is sufficient to carry away some heat (or use heatsinks for the LEDs). Otherwise, I wouldn't even attempt it as you'll risk your LEDs and maybe even whatever is around them. Play safe.