Thermal device and fan (integrate) 42W2821
I prefer the T61p fan, it cools very well on integrated and discrete boards.
NewModeUS ultrabay slim SATA Hard Drive Bay Adapter
If you'd like a genuine lenovo, I have some in new condition.
Intel C2E X9000 processor
I actually have one of these, but unless money is no concern, I wouldn't recommend it. A T9300 will give similar performance at 1/4th the cost or less.
T61 motherboard 42W7872 - is it really better to get this one instead of 42W7648? Because I'll have to flash Middleton BIOS anyway to get SATA2 working.
Good luck finding a 42w7872. It took me a year to find one myself, but when I did I got two at the same time.... haven't seen another since, but I keep looking, however if you are willing to spend enough money, I'm sure you'll find one, and since it looks like you're going to spend a few hundred dollars on a cpu, might as well put it in the right board. I do have a 42w7873 board if you want something with more powerful graphics, but the nVidia graphics do have some risk of failure, but the way I see it is when I build a computer like this, I don't want to settle for netbook class graphics. The Intel boards are nice, they run cool and are good for surfing the web, and general use, but on something like this with one of the best screens ever made, I'd want some graphic power behind it. I'm using an nVidia board in mine and keeping a spare handy just in case, but it really depends on what you're plans are. If you want to run it on battery a lot and you're not going to use it for gaming, graphic or video work, then the intel would be a good choice.
WLAN card - I want wireless N support. Which one is best to get?
I have no problem at all with 4965agn card. It's more then fast enough to stream 1080p video and run torrents at the same time.
PC Card/ExpressCard slot - FRU?
There are three basic models, pcmcia/express card, pcmcia/smart card, pcmcia/4in1 card reader.
I went with the first, but recently picked up one with the 4in1 reader. Since I've never used my express card slot, I'm going to install that next time I tear the system down.
As far as providing parts, besides the genuine ultrabay sata adapters and rare penryn/nVidia boards, I have a couple T61p heatsink/fan assemblies. I'd also be glad to help if you have any questions, but it sounds like you're already on the road to building a pretty amazing frankNpad.