To fix the question marks on folders, see: http://www.computer-darkroom.com/lr2_find_folder/find-folder.htm
These question marks really shouldn't have anything to do with the upgrade to Lightroom 6. Did you, after working on the photos in Lightroom 5, use your operating system to move or rename the photos (or the folders that contain them)?
I had not thought about it but I did move files, however I was very careful (because I didn't want to move anything outside of LR - knew this would cause problems) and got a video from Adobe explaining how to move the files (very similar to the wording in the link you gave. They all moved well in LR5 and are set up as they should be, but the LR 6 didn't get the message. Is there a way to sync the 2 LRs? Do I have to go in for all of the files I moved and follow the info on the link when all of the files are fine in LR5?
If your Lightroom 5 catalog is working properly, then open Lightroom 6 and select File->Open Catalog and point it to the properly working Lightroom 5 catalog.