Hi Notso, and welcome. I'm a relative newbie also (started 2 months ago), but I can at least answer two of your questions easily:
2. FPS measurement Q: pressing Ctrl+Pause will display an FPS counter on the top left of your display. Pressing a second time will include more frametime data etc. Pressing a third time will switch it off.
3. Flight Controls setup Q: I have the Thrustmaster 16000M and I only used the TARGET software initially to ensure all the buttons etc were operational. After that, I have no use for it.
Button mapping should be done in DCS, and must be done for each aircraft. However, you can import profiles (as well as save etc) in the Control tab under Settings. Just remember that throttle and stick profiles are saved separately:
e.g. to import a saved throttle mapping, click the settings cog icon, select the controls tab and select the appropriate aircraft from the drop-down. Click anywhere in the throttle column before selecting a profile to import. Same for the stick.
I would suggest looking at any of the Grim Reaper Youtube tutorial vids, as he shows button mapping for whatever aircraft is the topic:
https://www.youtube.com/channel/UCZuXjkFY00p1ga3UyCBbR2w/playlists?view=50&sort=dd&shelf_id=5
Hope my novice info helps. :)
