The 1624 has 8 internal A/D channels, so you can only record 8 channels at a time with the internal converters. Use external converter boxes to fly data in via lightpipe, and you can record all 16 at once. Channel count is not affected by bit depth. However, if you want to work at 24/96, you do effectively reduce the machine to an 8-track machine, whether you are using the internal converters or not (due to disk bandwidth limitations).
The base 1624 works very well with MTC sync, right out of the box. The 824/1624 does come with word clock I/O by default- it is not an option. I set mine up to be the master, and slave Cubase to it via MTC, using the 1624's word clock out as the system clock for my Hammerfall. It is seamless. Haven't really tried using the 1624 as the slave yet, but didn't have very good results when I tried... Didn't try very hard, though, becuase in my working model the 1624 is the primary recorder, and Cubase is just a curiosity.
The add-in sync option is SMPTE/LTC sync specific, and I don't have it. It only seems germane if you plan to do a lot of sync-to-video work, which holds no interest for me.
You can buy the HDD cradles from Fostex- I have 4 all told, and they are about $60 each from there. I'm sure that this is just a standard item, and someone with time to dig through Computer Shopper could find them significantly cheaper. I had a couple of projects that were hot at the time, so I just called up Fostex Parts and ordered them: 800-936-7839, and ask for Maggie. You can also just reuse the one that comes with it (they simply snap together around the drive), but I get in a hurry when I need to change projects, so I like to keep them ready to just slam in.
Actually, if I'd had more time while I was in there doing my acoustic noise reduction work, I would have changed out the drive carrier for a more standard one, like the Kanguru. The drive mount is absolutely a normal, industry-standard 3.5"-into-5.25" piece, so you could swap it for one of the more bulletproof aluminum units for road work, better cooling, or whatnot. The machine is really very simple and straightforward mechanically, so you're hardly stuck with their choice of carriers.
For more info on my noise reduction mods, see
http://www.homerecording.com/bbs/showthread.php?threadid=19703