One is under Audio the "Album" selection has suddenly disappeared.
Weird. That view is locked and should't be very easy to delete. You can recreate it if you want. Or you can drop your library, make a new one, and import your media again. Or reinstall MC30 again and import your media again. That shouldn't happen, but I'm guessing it was just some kind of "fat finger" type mistake where you pressed delete accidentally or something.
Also when I try and import the wav folder for example JJ Cale “Naturally”. It splits it into 2 albums.
That's a common "problem" with MC with some albums. Take a look at the [Artist] field on each song. They are probably not all the same. Probably one of them is different. Thus MC thinks they are two different albums. The fix is one of two things:
1. Make the [Artist] field the same for all songs. This is the correct fix if there is a subtle typo or similar and the album really does have only ONE artist for all songs.
2. If it's a compilation album, or has individual guest artists credited on an album that has one major artist, then you should set the [Album Artist] tag for all songs to be a single value. A good example of this is Santana's album "Supernatural". It's a Santana album so he is the [Album Artist]. But every song has a guest artist and the [Artist] field is set to those individual artists for each song.
See this article for more information:
https://wiki.jriver.com/index.php/Album_Artist_and_Album_Artist_(Auto)
Also with over 3,500 wav albums / folders, I would love to bulk look up and add folder.jpg Album Art as well as the basic Tag info including Genre to each album folder.
So your collection has no metadata at all? I don't have much experience with using MC for doing metadata lookups. MC has "Library Tools > Lookup information from online database". But I've almost never used it. If you try, try it with one or two songs. Then an album or two. See how it works.
Album art is a bit easier. Highlight some files or albums. Then do "Cover Art > Get from internet". That will give you choices for each album. It's pretty fast. I suggest doing no more than about 20 (albums) in a batch. Give it a try with one. Then do a few more. Then do a batch. The idea being that you don't want to get confused and do something you aren't sure about.
You probably want to make sure your cover art settings are set the way you want BEFORE you start. Tools > Options > File Location > Cover Art.
Audio mode: I like "same folder as the file".
Also store image in the file's tag: This writes the cover art INSIDE the audio file if it supports it. FLACs support it for sure. I don't know about WAVs but I suspect they do not support this.
When I first got MC and started importing and tagging and things my tags weren't great. What I figured out is this: MC gave me much more visibility into my collection. It showed me things that were wrong. I wanted everything to be as well tagged as I could reasonably do. So I spent quite a bit of time fixing things. Then I spent lots of time ripping new things and making sure they were correct as I ripped and imported them. This is the big thing: To do ongoing maintenance of your collection as you build it.
Starting with such a large untagged collection is probably going to be kinda hard. It might be quite time consuming. The question is, do you want a well tagged and curated collection? If so, you must become your own digital librarian. You are in charge. The level of detail and attention are up to you.
Good luck to you.
Brian.