I think you are on the right track get all your agents done first
We are running agent version 3.0.2.03 and 2.3.09 with our 5.3.1 master (windows) but I don't think 6X supports any 2X agent
We added an agent but didn't add it to any agent lists and did testing with different "jobs" with the higher rev agents in a non-prod environment.
I ran into issues with native tidal FTP MGET jobs when the targets have large amounts of files on them (one providor in our case). The MGET can potentially timeout and complete abnormally... . I had opened a case SR 620663441 earlier this year and I felt we proved that the FTP software they use does a list BEFORE it does the MGET (which is the problem). I am not sure Cisco considers this a "defect" and don't get the feeling this will be fixed.