I too have used TS2000 and Flex6xxx and am working from a screenshot of my 1.3 CAT settings and I just cannot get it to work.
my HRD Logbook).
I copied the program from http://sourceforge.net/projects/jtsdk/files/win32/2.0.0/wsjt-suite/
and it runs without installing.
I can always switch back to 1.3 if I find problems.
I've been using my Flex-6300 to make a lot of JT65 and JT9 contacts. My flavor of choice is WSJT-X 1.2 which works very well using DXLab's commander for rig control and DXKeeper for logging via JTAlert. I also have WSJT-X 1.4rc4 working using TS-480 for rig control (Commander is NO LONGER available.. sigh), and all rig functions work fine. However, the Wide Graph input level does not answer to the main screen's input level slider as it used to, you need to use the separate controls on the Wide Graph itself (which I can get used to), but there seems to be an additional base line signal added on to the input signals from the Flex that are annoying to say the least. This add on signal does not appear on the Flex water fall, but does appear in the Wide Graph waterfall.. If anyone knows where this strange signal comes from and how to get rid of it, I'm all ears. I have screen shots and wav files that show its not there in 1.2, but is present in 1.4rc4, and I have sent them to Joe Taylor.
73, Doug AK4HB