In trying to fix my skin deformations, I noticed a couple problems in my script when dealing with vertebra connections. Namely, their attribute files were pointing to specifically numbered vertebra and it needed to look at them to determine which number they were. This worked great when I had parts of the same animal and the entirety of the animal was in the scene. This didn't work so great when I was just working with say, a torso and an abdomen, and it needed to look at the neck. Anyhow, I changed the vertebrate naming convention and the way the script worked to fix this problem. In the process, I broke my script, so that took me a couple days to fix. Not fun at all.
On the up side, I got the border extrusion stuff working much quicker than expected. As I thought, Maya's default border extrusion caused me problems. Borders were flipping, edges were rotating, and worst of all, it didn't maintain the edge numbering at the border (which basically would have broken any future connection attempts). So I made my own extrusion that basically evenly spaces out the curve along its length and then moves the border along this spacing, inserting a new edge loop between it and its immediate neighbor with each move. By doing this first and then running the standard skin deformer I use for all bones, I managed to get really nice results.
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