I've made a mesh and followed the instructions of lthis tutorial but every time I test the mesh in game it completely ignores the morph files I've generated.
What are some common problems with morphs that could be causing this? It seems to happen when I start using applying LOD models, I made a testmesh with only 1 LOD level and that one morphed fine.

Is the mesh a accessory or an actual clothing Mesh? because this seems to be more like a 'manually adding' your morphs to it. I guess you could try Meshtoolkit for adding morphs. Though, I should check if you did the comments in your morph meshes correctly. That could be the main cause of the issue.

the comments in my meshes should definitely be correct, for the base I copied it from the source mesh and for the morphs I used this;
FVFItems: 3
TableType: 0
References: 1
TGIRef00: 00000000 00000000 00000000 00000000

Is it possible that a tiny mesh with a significant amount of verts close together could be the problem?

Hmm, from experience, if it was really close to the mesh, it won't be really visible to 'slide' like if you look at the morphs of clothing, it's usually that there is at least somewhat space to it, so it's visible when sliding. Now if you're making necklaces, you won't really see it since the sim's neck doesn't really change much.
The only thing that could be the issue with a lot of verts would be a really spike-y creation.

Are you making a clothing mesh or an accessory?

I'm making a piercing accessory because I thought it would be an easy project to learn about morphs , since I would only have to move it
Something like the image below.

I somehow got it to work now, I even got the LODs to work. I wish i knew what was causing the problem initially though

Glad you got it working! ^.^ I think it was just some data that didn't come through to the game. I had the same issue with a hairstyle once that I made through daboobs. Morphs are really a pain to work with if you're doing it the manual way >-<

So there's a way to automate it with TSRW? I did this with CTU and meshtoolkit

Yep! I use it regulary on clothing. On piercings like these, I would try to do it your way, as Meshtoolkit and morphing stuff like that automatically aren't always... well... good looking. For clothing this is very helpful. All you need to do with TSRW and meshtoolkit is, cloning EA's mesh. If you have nooo idea how to do that or too much effort or just doesn't like taking up too much space on your own computer, you could take my exported WSO reference files. They have bones and morphs. : http://simfileshare.net/download/39787/

Now basically what you need to do is, making sure you have a 'group_base' instead of 'geom_00' or something else. Else TSRW and meshtoolkit won't see your morphs correctly. Or actually, won't even read them. Make sure you finished your own mesh in MIlkshape with neck seams fixes, and all these other issues, export it as .WSO

Now open up Meshtoolkit, and there you will see multiple tabs. Click the 'Auto tools for WSO'. There you see 2 tabs, which both work the same way and you both want to use one by one.
The tag saying 'WSO mesh to modify = YOUR MESH" So locate your own WSO file in that bar.
the 'Reference mesh' = the exported EA mesh. Or, WSO files from my folder.
Make sure when you use a reference mesh that if you have a female body You use a female body reference. ALSO make sure if you have a full body mesh, you take the 'Full body mesh' reference.

Then say you did it in the Bones assign tab first, you can just simply replace the WSO file that you need to save with yours. And when you do the exact same thing in the Moprph adding tabs, Make sure you select your edited mesh that you just ran through bones assign tab in the 'WSO mesh to modify' then replace it the same way as you would with the bone assign tab.

Thanks, I'll definitely give that a try if I make some clothes