[3DS Max?] Rigging's a tad messed up on my model

Hello everybody! I’ve been having an issue as of recent with a character named ‘Temperantia’. In the pictures below, there’s two different models: The completed, unedited version and the one that is complete but with parts removed (the meaty bits you can see in the unedited version)

Edited Version (What it looks live before toying with it)

http://i.imgur.com/C049MbJ.png[/T]

Edited Version (After moving any of the head bones)
[T]http://i.imgur.com/kg4Qols.png[/T]

Unedited Version (After moving any of the head bones, it’s not really obvious but you can see some of the neck morping)
[T]http://i.imgur.com/1U3jltG.png

As you can see, in the edited version there’s some meaty bits that are there when they are all removed (save for one part i forgot to highlight) and it’s evident that some of the rigging is less than… satisfactory. What I did in that model is I first highlighted each of the unbroken pieces of his face (that means his face, eyes, nostrils, eyelids, the sphere, the neck, all that stuff) using the Edit Mesh. The reason I use Edit Mesh is because I actually put together model which was all in .PSK files. After the pieces were all put together, I proceeded to then re-export it as a .dae file which seemed to work fine. However, because of .PSKs tendencies to merge meshes, I had to put in Edit Mesh via the dropdown in 3DS Max.

Anyhow, I highlighted the pieces I didn’t want deleted and then used Hide Meshes, leaving the meaty bits and broken up pieces. I hit CTRL + A on the rest of them, deleted them, and then unhid the meshes. Everything looked normal, the export went fine, but that happens then. I know it has to do with the Edit Mesh part somehow, I’m just not quite sure how. Can anybody help me out on this problem, please? I’d much appreciate it.

And if anybody needs to know, I’m using 3DS Max 2012.

Thanks in advance! Sorry for the length post.