Brandon,

I tried replying to the galaxy userlist but it said its for authorized users only, and i asked for permission but no response yet.

You can manage your subscription to galaxy-user here: http://lists.bx.psu.edu/listinfo/galaxy-user/

I just had one quick question, the output files from of CDS diff, promoters diff and splicing diff from cuffdiff only report have sqrt(JS), teststat, and p value stats?

Correct. You can find full details of Cuffdiff's outputs in the manual: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output J.