Nikki, I'm a little confused here...why would you get the G5 with the 9600 and then purchase the 9800 ME retail edition? You aren't going to save yourself any money from what I can see - the BTO 9800 with the ADC connection is an extra $300, and the retail edition of the 9800 without the ADC connection is $364 minimum AND you will then need the ADC to DVI converter...
I don't know what you'll be able to sell the 9600 for (PC versions are going on eBay for $139) but there might be issues of whether or not things fit. If the 9600 Mac Edition is available ONLY for the G5, and looking at ATI's web site, I believe this is true, it's quite possible, looking at the Barefeat's article, that it won't fit in anything but a G5, which makes your market a tad small (only those who bought the non-dual G5's with NVidia cards who now want to upgrade). The article quotes ATI saying that the ONLY cards that fit both G4's and G5's are the Radeon 9800 retail versions.
I think your best bet is to get the BTO G5 version of the 9800....not sure about the fan issue (the G5's are incredibly quiet with their own video cards) and if S-video is needed, the adapters for DVI to S-video/composite-enabled devices are $19 from Apple.
Just my 2¢.