I can't believe I missed this thread the first time through!
I have been wanting to do something similar and acquired my case donor, motherboard, and 8.4" color LCD last April or May, but other than acquiring parts, I haven't made any progress.
So far what I have is a pile of parts sitting on a desk that boots OS X Leopard 10.5.6. I'm using a Jetway J9F2-KHDE Mini-ITX board and a small 150W PSU. I'm using a iMate Griffin so I can reuse the original keyboard... I could reuse the original mouse too, but I'm too addicted to scroll-wheels and right-clicks to use the original mouse. I may buy a Mighty Mouse just to keep everything Apple.
On mine, I'm leaning towards mounting the motherboard low in the same place as the original, and carefully cutting out a perfect rectangle in the rear for the I/O shield. If it looks clean enough, I'm not sure there's a lot of value in preserving the original port holes.
I've been wishy-washy on the screen. I bought an 8.4" color LCD, but I kind of like the retro look of the original B&W CRT. I have had thoughts about building a custom CRT board with grayscale video amp based on a schematic I downloaded from here, and finding a way to mod the analog board to accept VGA sync. Perhaps boosting horizontal deflection voltage is enough to accomplish this? Based on what vague information I've been able to find on the Color Classic VGA mod, all they did was boost horizontal deflection voltage. If there was much more done than that, they failed to mention it. I'm not too worried about the low resolution of VGA since I'll be using a 24" LCD as a primary and the internal screen will just be a secondary.
I'm also not sure cutting the front off a CRT to use with an LCD is the best idea. My LCD has an anti-glare coating, and so does the CRT. Wouldn't doubling-up on the anti-glare result in a blurry LCD? I have that concern, and also feel bad about cutting up a perfectly good CRT. An alternate idea I had is to get a piece of clear plexiglass (Lexan), place it over the face of the original CRT, and heat it up with a heat gun. It should (in theory) soften and form to the shape of the CRT. Then use that as a lens on top of the LCD. This would result in a shiny and not entirely authentic appearance, but should still match the aesthetics I think.
Anyway, cool project, keep us updated on how you decide to proceed. It may help me make up my own mind on my own project!