Hiya!
As a HHKB I can deefinitely recommend this keyboard to anyone who asks. However, it is of course all personal preference (hadn't seen that one coming, had ya!).
1. Yes, it is very comfortable. It has a nice tactile feedback, and it got the right amount of force needed for actuation to be easily for hours on end. However, I simply don't like topre, and just switched back to cherry mx.
2. When you mention the JD40 and the size of it. You probably know this, but do remember that everything on the keyboard is "standard" size, with same gap between keys etc. So in terms of that, it wouldn't feel any different to other leyboards with a more conventional form factor. You might have to take into consideration the lack of dedicated number, f-keys, arrowkeys and so on though!
3. I'm in the same boat as you on that. I love how the HHKB looks, and especially the black ones ^.^
As for the bluetooth; there are a few mods you can do to make your HHKB work wireless with bluetooth, but I don't know much bout that.
I would highly recommend the HHKB, and it's a great board (I for one, love the layout and form factor). I can't really comment on the thinkpad-HHKB relation though, since I've never used a thinkpad
) Do also bear in mind that the HHKB is just as noisy as any other mech, it just has a slightly different sound to it.
Can't comment much regarding the JD40. I love how it looks, and I think it's awesome, but I don't have one!
As another option to the HHKB I would recommend the Poker 2, which you probably already know about. I went from the HHKB to a Poker 2, and so far I'm enjoying the Poker way more. That's mostly 'cause of switch preference though!
EDIT: I wrote this whole thing on my phone, and somehow a lot of stuff got cut out O.o that's why some sentences might not make too luch sense. Sorry bout that! I'll probably fix it later.