Devon,
This may be a dumb question but how did you do the v.2x to v.3.6 migration? I had an older version running and had to spin up a dev VM, install the newest Flex Viewer app, copy all my old projects from wwwroot to the new flexviewer folder under wwwroot on the new VM, then my 3.6 flex viewer application was able to see all the legacy web maps. I then hit upgrade on each one, some of the tools had to be completely replaced with new stuff. Its been a major time suck. Especially with like 45 web apps running. I would look at that if you have time and haven't already.
My second observation is that after downloading the two xml and looking at it in Notepadd++, you are comparing apples to oranges in my opinion. With 15kb worth of additional text, I am sure there can be a half dozen possibilities with regard to whats causing the error.
Good luck man.