Upgrading Unity from 5.1 to 5.3.4 has broken game, specifically models made in Blender

I recently decided to upgrade Unity after putting it off for some time as I have a rather sizable project started in 5.1. I knew there would be some hurdles, however, I have had very little luck in getting the game back up and running in the new version. My Blender model animations seem to be gone and many of the faces are disappearing. For example a characters arm is just missing and other similar issues across models. The warning I'm getting seems to be due, at least in part, to a shader I'm using attached to a prefab, however, when I change it to even the standard shader Im still getting the warnings and the issues persist.

My question is: Is there something I'm missing in the upgrade process that can make the transition easier, because right now, it would seem I need to recreate all of my Blender assets and reassign all of my materials and not be able to use some of my shaders?

The process in which I upgraded was very simple. I just opened the project folder with the new version of Unity and rebuilt the project for the new version.

Any help from anyone who has experience migrating projects between different versions of Unity would be appreciated.

• Try closing Unity, deleting your Library folder, then re-launching the editor. It will regenerate all the data from your source files. This can sometimes resolve data corruption errors. – DMGregory Apr 26 '16 at 12:23
• @DMGregory Tried this, unfortunately it did not fix the errors. I can't even find a way to see which shaders are causing the errors. – GeoJohn Apr 26 '16 at 19:34