[Richard Rodriguez]"Have a client that wants everything exported from FCP HD into flv's @ 960x540. "
Do they mean FLV or Flash. FLV is Flash 7 (Sorenson Spark/H.263) and Flash 8 (On2VP6 S and E).
Flash 9 can be F4V, MOV, MP4 (All are H.264 and they all work in Flash Players and can be used in Flash for interactivity)
The answer will determine which direction you take.
If Flash 9 you can do that in Quicktime and Compressor as is. H.264 .MOV works fine and Adobe has said there is no current difference between that and F4V. It's been compatible with Flash since Player 9 Update 3 December 2007. H.264 is used by YouTube, Vimeo, Hulu use for HD.
Some people use H.264 in FLV as well but Adobe does NOT recommend that as it may not be compatible as things change.
They're OK with Flash 9? Don't assume. Ask the client unless you feel they'll accept your decision. There are still some who insist on Flash 8 (which would require a purchase).
It depends on the typical target and the content. YouTube is doing 1280x720 at about 2000kbps for example so to get similar quality at 960x540 you might try around 1200kbps but it really depends on content. You can try the Compressor Apple/Web/QT7 compatible (which is also Flash 9 compatible) H.264 LAN preset and copy and modify aspect ratio and modify Frame Controls if you need to deinterlace.