In the days when backups worked and you could replace purchased apps from Nokia Store I would probably have suggested re-installing device firmware but only as a last resort now. Hope you got a decent quality replacement screen as some poor examples around; if you long press on "Messages" icon do you get "Done" & "New Folder" just to check this particular spot on touchscreen working?

I have one N9 with annoying screen fault as can't use Filebox in "Portrait mode" as bottom right corner of touchscreen defective (portrait), so have to use in landscape mode so icon has moved to what was bottom left corner when rotated through 90 degrees if this makes sense to you.