Not much of an update, I can't really decide which I prefer after over a month. FWIW, my usage consists of writing LaTeX, C, Java, browsing, and playing some games.
I made the following layout modifications to each of the boards:
[ Attachment Invalid Or Does Not Exist ] 46529[/ATTACH]
[ Attachment Invalid Or Does Not Exist ] 46530[/ATTACH]
I found the arrow layout not as bad as I had feared, but still rather frustrating at times. I mapped a traditional inverted T on the right side of the board, at the expense of displacing a few surrounding keys. I really like the new location of the  keys for coding, and feel much more comfortable overall with this layout. The major drawback is accidental up arrow key presses in text editors, when you meant to hit comma, but this was a surprisingly easy adjustment.
I swapped the -/+ keys to be consistent with the TE, and because TE's arrangement is slightly more intuitive to me there. When gaming with the arrow keys, the fingers sometimes catch where the keys meet the case, as there is little clearance there. This does not happen when pressing the arrows from the home row position, and the fact that they may be easily and intuitively pressed without leaving the home row is a definite advantage over the TE, as is the thumb delete key.
The major downsides of the Kinesis are the tendency to mix up the lower two rows, and the function keys.
Despite the overall height of the board, the home row is only slightly higher than on a standard board, so my Logitech Marble "Mouse" sits at a comfortable height without being propped up, but needs either to be placed about 1cm further right or 1cm further up than with a conventional keyboard in order for the thumb to clear the case. This is negligible, and I prefer not to prop it up.
In theory, their layout of Shift, Control, and Alt makes perfect sense to me. In practice, it drove me absolutely insane in the course of writing a 2 page LaTeX document. The moment I swapped Shift<->Control, I started to enjoy the keyboard much more (I was already used to the Unix Control position on the left side). The directional clusters require slightly more hand movement to use, but I don't tend to inadvertently hit keys on the wrong rows as I sometimes do on the Kinesis. The left navigation cluster, while intuitive, is slightly less so than I thought it would be, simply because I'm used to performing all navigation with the right hand. The Navigation clusters can be hit with the thumbs to some degree from the home row position, but not as readily as on the Kinesis.
From pictures, the thumb enter key looked a tad uncomfortable as it is not angled like the space bars are. In practice, I have not noticed any discomfort from this, though adopting the space bars' angle for this key would be preferable.
I thought I would prefer the TE's narrower stance for "mousing", but in practice I'm pretty ambivalent about this.
Many are leery of adopting alternative, ergonomic layouts as they interact with a myriad computer systems, including laptops, and don't want the hassle of switching layouts and such. This is a legitimate concern. I don't have much trouble typing on standard keyboards now and then, but I do catch myself trying to use the spacebar as backspace, enter, and such. If I were forced to use standard layouts the majority of the time, I think I'd just stick with a Filco Tenkeyless at home for consistency.
Ripster suggested a while back that having one's keyboard at the correct height is far more important than having an ergo board, and I tend to agree. I've used a height adjustable sit/stand desk for a couple of years now, so always have my keyboards at the right height, with my hands hovering as I type. I feel that this and going tenkeyless made a much bigger difference to my comfort than did the subsequent transition to TE/Kinesis boards. I have never had any serious RSI issues however, so YMMV.
Both of these boards are great, and for those of us who don't mind the alternative layout, they are well worth the investment, and I think they work well even for programming, provided you tweak the layout to your liking. I'm quite happy with both boards, but just wanted to give some perspective....