I'll let someone that actually has dealt with a 100 system rollout answer the first question.
The size of the old client's (wu) was about 23k; I'd assume the size of the packet hasn't increased much if any. (haven't looked at the size of the files that disappear for each generation)
I noticed my AXP 1800+ system finishing generation in around 5 days. (add a day or two if the system gets hung up alot; I got stuck on a generation for over a day - and another fellow got stuck for 2 days). Verify the actual (wu) size, and you can estimate how many get sent by estimating how much faster/slower your system is than my AXP 1800+ with 256Megs with the "use extra ram" switch under win98se.
For scheduled uploads - you can run with the "nonet" switch, then stop the client and run with the "upload" switch, then switch back to "nonet". List your machine operating systems; and perhaps folks here have scripts/batchfiles they've written to help out. Take a look at dFQ - which supports collecting from large groups of nonet machines, uploading from a single internet connected system - and see if it has scheduling abilities.
I've seen a few folks using a variety of ways of monitoring their windows systems; are you running WinNT (4.0, 2k, XP), Win9x (95, 98, ME), Mac, Unix/Linux etc? Mention the operating systems run by the slaves, and we'll get a few suggestions for you.
Under windows, you have the option of running the client in Quiet mode. (an active black screen box appears). It can be run hidden. (supposedly the black box disappears). And for WinNT (4.0, 2k, XP) it can be run as a service, and it doesn't show up on the desktop.
The readme text file has a description of the switches mentioned here; and how to run the foldtrajlite.exe /install to set it up as a service.
Granted.. I cheat and use dfGUI 3.01 to setup the command line switches in either service.cfg (for the service), or foldit.bat (for the text client).
(hopefully, this will con a few people into filling in the blanks I left..
Good luck..