Wow, 3,000 sources in a 10,000 database. I only have 531 sources in my 30,000+ database...anyway to answer your questions.
1. Free notes are imported into TMG as a source.The problem is that since they have no sturcture like the standart sources in UFT, nothing is put into the full footnote text, short footnote text, or bibliography text in TMG therefore would not show in you notes to a report.There is a procedure that someone has come up with that easily fixes it in TMG but you have to edit each one in TMG, in your case, a hundred.So it's your choice, change them in UFT or edit them in TMG.I'm sure that procedure will be published in the newsletter and probably posted to the board once the beta testing is over.
2. There is an import option "Construct footnotes using imported rules (componets syntex). If off, TMG Reference Manual page 267 applies).You will want to check this item on the import option screen to let TMG take the footnote text structure of UFT and put into the TMG footnote text.