Hi,
1. The plugin only override EDD download button to every download with price of 0, so it doesn't have anything to do with the upload method, if you succeed to upload them as EDD download item, then EDD Free Download should works.
2. Under EDD Settings -> Misc -> Free Download Settings, you can edit the Download button text, with the latest version (0.1.9), you can use %name% wildcard that will be replaced with the download title.
3. Can you please elaborate on what links did you meant?
4. The plugin only add 1 statistic in the backend, that is download count under All Downloads listing page, it's not showed at the front at all, and currently there is no option to hide it in the backend.
5. Hmm, I am not familiar with that plugin, from a quick look, I can't see that it will conflict with this plugin, but you will need to test it yourself.
And you may want to ask some of your questions to EDD support forum (especially question #1, #4), since I think you will get a better answer there.