It looks like mzXML files created from .t2d files using that conversion tool will not be compatible with the CPAS pipeline without some work on one end or the other. The mzXML file that you posted does validate against the mzXML schema. And after minor manipulation, I was able to read the data encoded in the mzXML file.
However, there are a couple of issues with the file. The first is that there are no line breaks whatsoever in the file. In theory this shouldn't matter as it's XML but in practice it does break programs that try to read the file (like Tandem). The second problem is that even after adding in the line breaks, the peak lists are encoded in 64-bits whereas Tandem (and a lot of other tools) are only capable of reading 32-bit encoded peak lists. Thirdly, the resulting file indicates that it's an MS/MS scan (scan level 2) but the mzXML file contains no precursor peak associated with this scan. So even if the other issues are dealt with, there's no way to associate a peptide mass with this MS/MS spectrum so it can't be searched using something like Tandem. I will email the converter developer (from U. Michigan) to see if he might have time to modify his tool; the alternative is to update Tandem and possibly CPAS to handle files like this. The t2d converter is open source so you might be able to address these issues yourself if you're a developer.
Lastly, your question about what FASTA file to use implies you're new to MS-based proteomics analysis (as it's a question that can't be answered w/o other information that you haven't provided). I would suggest that you interact with the person who gave you the t2d file and get some guidance and background from him/her. Good luck.
error.txt
G24_MSMS_1614.9180_11.t2d.mzXML