I cannot simply let you go on the quote of saying the HHKB JP is tiny
Ah ah, I agree with you... I always hit it at the same spot indeed and now, after reading your message, I think that it's quite large enough!
I've got three more quick questions for you...
I apologise if sort of ripped you a new hole. I have seen too many people complain/moan about HHKB JP's small spacebar that basically bottled up my rage and eventually let it all out.
The issue is trivial but when thinking about it, it can probably help deter people wanting to borrow your keyboard for instance when they see the small spacebar.
The thumb only needs to hit the spacebar
As I wrote: my right-thumb, yes. The space and only the spacebar and I only ever use my right-thumb to hit the spacebar (I know some people do alternate thumbs on the spacebar, like the true gods of touch-typing did envision it... But I'm a pagan from that standpoint: I do still believe in the touch-typing religion, but I only use my right thumb to hit the spacebar and that's not gonna change).
Which then means my left thumb is free. Which is precisely why I want modifiers closer to the spacebar: because the finger I use to press the modifier at the left of the spacebar (called 'diamond' or whatever on my HHKB Pro 2) is my left-thumb. So the closer the modifiers to the center, the faster and the more comfortable it is for me to hit it.
I'd follow Oobly's hint to try an ErgoDox but sadly after 30 years on staggered keyboards I simply cannot adapt to matrix layout (I tried very hard on my shiny R&D white ALPS split matrix board but simply can't. I just can't. My brain has been permanently damaged and matrix layouts aren't for me. Moreover I want something close enough to the non-ergonomic keyboards that I've always used. And, no, stop PM'ing about that R&D board: I'm not selling it ; )
Are all the HHKB Professional JP using Topre switches? For example I like the black "Happy Hacking Keyboard Professional JP 墨 PD-KB420B" at about 19800 JPY / 192 USD / 143 Euros.
Of course it has the "weird" ISO like Enter key but I don't care much about that anymore: I'm basically only using the physical subset of keys common to both ANSI and ISO keyboards (and now I'm happily mixing ANSI and ISO keyboards in my collection).
Having stuff shipped from Japan to me ain't an issue: I've got a contact in Japan coming once in a while to my country (that's how I got my HHKB Pro 2)
The coneco.net site you gave seems to be cheaper than amazon.co.jp (which is the one I typically use): is coneco.net known to be cheaper than amazon.co.jp? (but my contact has free shipping to Japan on amazon.co.jp, don't know about coneco.net)
Would you recommend the silent version? (I'm happy with my regular HHKB Pro 2 and before that I had floss-modded Model Ms so I take it it's not that important)
Do you know how the references work for the silent / non-silent version and Topre / non-Topre version? For example is PD-KB420B going to be silent or not? (I think the last 'B' is for 'Black' but besides that I'm not too sure).
Thanks for your very long message... Seen that I like Topre I think I'll got the HHKB JP route: I was asking here in case something else existed... In case the Filco minila existed with Topre I would have bought that: there are going to be many keys I won't be using on the HHKB JP and it just seems a bit "weird" to buy a keyboard with many unnecessary keys but whatever
Yeah when I switched to my HHKB JP, I realised I hit the spacebar more often with my right thumb than my left. Though at the same time I guess I should also try practising hitting the spacebar more with my left thumb. With my HHKB JP now, I guess the need to flex those thumbs around a bit more and or to use fingers on other positions for cases where such keys did not exist once in ISO/ANSI layout. I guess at this rate I am also on the same level as you, a pagan.
I personally have never tried the matrix (grid like) layout, so for me to try something learning that would probably be as difficult as it is right now for me when I have deliberately mapped my keyboard as a JIS keyboard. Meaning whatever characters I see on my HHKB JP, if I were to hit it I get exactly that character instead of whatever it was for the ISO/ANSI layout. So far it has been somewhat a bit of a struggle, so I too can imagine if I were to eventually swich to matrix layout keyboard.
Can you sell me your R&D white ALPS split matrix keyboard please?

*kidding*
Now onto your questions:
Answer 1: As far as I know of all HHKB Pro are Topre based. I don't think PFU would try and confuse one even more further by mixing Topre with membrane keyboard. Hint, from the links that I posted before if you were to omit the words Professional, you would see the prices of the Lite2 variants. There is at least a gap of about three times the price difference between a Lite2 versus any Professional. Even wikipedia for instance would label that as well:
http://en.wikipedia.org/wiki/Happy_Hacking_Keyboard#Features_by_model The model number scheme is quite different at that.
Yeah the weird ISO like enter key is the same as with virtually any JIS keyboards. I guess JIS keyboards somewhat loosely follows the ISO layout but instead swapping a few keys here and there and adding extra keys. I too have a mixture of ISO as well as ANSI layout boards though it seems like I am more well versed with ISO layout than ANSI.
Answer 2: coneco.net is the same as kakaku.com. All they are, are just price aggregators, they aren't a shop but they list the prices of shops for instance that would sell the same product.
For a shop to list their prices lower than amazon I guess is quite rare. It is almost like as if the shop is wanting to battle against the "goliath". In any case the price may not last that long for that shop or otherwise I would start questioning the genuine factor of the same product.
hasu who wrote and now maintains the TMK firmware as well as one of the people that I see is residing in Japan even recommended amazon.co.jp for usually the best price:
http://geekhack.org/index.php?topic=47559.msg1078907#msg1078907Aesthetically, the site layout is similar to that of found on amazon. So for them to list amazon but not of another similar site that aggregates prices would be the norm I guess.
Answer 3: Type-S or not subject still remains hot amazingly enough. It ultimately boils down to personal preferences. I have sort of went through the differences on Type-S versus standard in another thread:
http://geekhack.org/index.php?topic=51598.0I also have made my reasonings fairly clear with my HHKB purchase on my own created thread (hint: my signature contains a link), the reasons also include why I prefer Type-S as well.
What I didn't realise until later was that people whom bought their HHKB from elitekeyboards for instance are allowed to return it if there was a defect or something with the said product. Buying for instance HHKB JP does not have that option as I have mentioned that in my post above for Type-S comparison.
To have factory fitted silencing I guess with warranty gives one the option to return it back to manufacturer if there was an issue within a year worth of use, of course to retro fit silencing when your keyboard does not have that by default would most likely instantly void warranty if applicable. However the case again does not apply to HHKB JP as far as I know. HHKB JP cannot be sourced from elitekeyboards so that means the only choice is to source it directly from Japan.
As for model numbering scheme, I am not an expert. Though it seems according to both that wikipedia link that I posted above along with deskthority wiki:
http://deskthority.net/wiki/Topre_OEM_Keyboards#Compact it seems the silenced variants are labelled with "S" on the model number. So in your case having the letter "B" apart from the numbers and whatever else just means that it is labelled, gray (or charcoal gray, not black actually) and not silenced. If it were to be silenced it would have something that ends with BS, and maybe blank and gray with silencing it would be BNS.
The model numbering scheme appears to be more consistent somewhat as of late on the Pro series.
I really do not know why PFU would designate charcoal gray professional keyboard as "B". It doesn't really mean black as a real black keyboard would be legendless consdering how either PFU/Realforce or whomever manufactured the key caps can only print black legends. In other words, black legends on black keyboard results in black and legendless keyboard. Maybe they want to keep using "B" in consistence with Lite2 variants?
Black Lite2 are really black but instead of having black legended keys, it is white. Whereas the black featured on the Professional series is more like gray with black lettering.
If you are curious, the Japanese word for black is 黒 (kuro/くろ). You can see that doesn't even look the exact same as 墨 (sumi/すみ) which according to Google translate, it means ink.
As for other keyboards with Topre switch, you will find that is a rare option. There aren't many manufacturers using Topre switches compared to Cherry MX switches. The case is even more magnified when it comes to 60% boards as PFU is the only manufacturer that I know of which still produces 60% keyboards with Topre layout (or maybe at least that they license the design to some other manufacturer). I personally wouldn't know of any other 60% keyboards that would have the features that you want whilst retaining the 60% layout and specifically HHKB style. A custom keyboard might do it otherwise.
I actually thought it is pretty amusing how at the beginning you stated on the thread that you don't want to go through the HHKB JP route and to have someone ultimately saying exactly just that. Otherwise I wouldn't have had any further worthy comments to add.