Spotlight index has ghost app that I cannot get rid of
The indexing is not finished, I would wait until it is finished before considering an error. 

If the indexing is still going on 2 days after the clean install, you either have a big drive with a lot of files or it's hung on something. That usually happens with wrong permissions on some files and in worse cases because of I/O errors of the drive. 

In order to check that you should take the following steps:

First: run the Disc Utility found in /Applications/Utilities/ to check your drive and repair permissions. Details for usage can be found on the Apple Support Pages found here

Next: I strongly suggest you rebuild the Spotlight Index in any case. A guide to do that can be found on the Apple Support Page here (In short: Click on the Apple Icon > Privacy > add your drive, confirm, then remove it again)

Most likely your problems will be solved after these steps.