I cannot give you answer to all your issues but I'll make suggestions about iTunes Match.
Firstly, if you should add iCloud status to your song view. Go menu > view > view options and tick iCloud status. This field will tell you the tracks that have been matched, uploaded, purchased, duplicate, inelligible or waiting.
You can then examine specifically those tracks marked duplicate, inelligible or waiting.
Duplicate is usually shown if match believes you already have that exact track in your library. If they are not try selecting track then ctrl click and select add to cloud.
Inelligible tracks - why? Must be music file 96 Kbps or greater or music video purchased from iTunes Store. Other will show inelligible.
Waiting - means tracks have not been matched or uploaded. Why are they still waiting - could be a problem with file.
I've done all of that. I keep the 2 iCloud colums always on my main screen but not in playlists.
On a different computer I'm running Araxis because I found an unnamed folder on my desktop ext HDD.
I imported them into iTunes under the same ID as this laptop. I have a MacBook Pro and MacBook Air. This is on my Air.
There's at least a minimum of 3+ copies of each song. I don't have iTunes open on it since running Araxis, but it did an iTunes Match and my nicely somewhat clean library on my Pro is now looking bad. But Match says I have 16,XXX songs....on my Pro.
Do I just need to clean up my MB Air Files and then iTunes and Match will be cleaned up too??
Is there a way to merge the two libraries into one since they are on 2 different hard drives. Just use home sharing??
Suggest that you use home sharing to transfer files that are not on your MacBook Pro from the Air. Once you've got them all on the MacBook Pro allow to up date.
Next use iTunes Match to show those with an Icloud Status as "duplicate". If you are happy that they are duplicates, delete them from your library. Next use iTunes to find exact duplicates. Under menu > view > you will see find duplicates - if you hold option key this will change to "find exact duplicates". You can now delete appropriate version.