I should think that it isn't as much a matter of the proximity of the hands as it is the unnatural angle of the wrists caused by this proximity. I use a 105(102)-key board and put the ZXCVB one key to the left which I feel greatly aids the left wrist's angle. I have no problems and feel comfortable, at least.

If you have the chance to get an angled, curved and/or maybe most importantly non-staggered keyboard, however - by all means, it should be good for you.

Your soreness, however, in all likelihood mainly stems from overdoing it with a new layout. You'll be tense because you're concentrating and you'll be prone to too long practice sessions. Make sure you work out all of the arms including your shoulders - pushups and shadow boxing should be great - and shake loose a lot. And be patient.

I got a CTS-like problem a few years ago, and the solution for me was a ergophysiotherapeutic training regime adapted to my physique by a specialist. The training increased the strength and circulation of my wrists, arms and shoulder areas, and the results were simply amazing! I haven't had any trouble after that, really (apart from a tension problem in one shoulder that came after I broke my collarbone - still working on that).

The middle two columns in colemak can cause strain, because some *moderately* common letters are placed there.  If they were more common, your fingers would be hovering there anyway.  And if they were less common, they wouldn't matter.   It's the moderateness of their frequency that hurts.

I think it's because of a weighting assumption in the Colemak design (I've seen these weights assumed for layouts other than Colemak too, so I'm not knocking Shai) where a lateral movement of the index finger is considered easier than vertical movement of any finger.   I found this wasn't true for me at least.  For instance, Colemak makes b tougher for me to type than x; d tougher than f; j tougher than semicolon; and g tougher than p.  In all these twosomes, the first letter is significantly more frequent than the second.  The following modification may be easier on your hands:

q w d f p ; l u y j
a r s t g h n e i o
z v b c x k m , . /

(The last zvbcx is due to the late lamented Leszek, lost now to Dvorak.)

All subjective, of course.

Hmm, you really don't like rolls that start outward and then change to inward (like 'ion' or 'rat' in Colemak)? Just wondering because you find 'eu' quite comfortable in the above layout; this would be 'io' in Colemak, so only the 'n' is missing to complete 'ion'. And the 'o' to 'n' transition is an inward roll, which most people find more comfortable than outward rolls.

Personally I find 'on' the above layout ('ue' in Colemak) above much worse (same finger).

Oh well, to each his own... :)