Recently, I've been working on this model that I imported into Blender from vg-resource.com. I'm no expert in Blender, just a beginner. The problem I'm faced with is when I attempt to parent with automatic weights, mesh to bones. The mesh turns 90 degrees on the Z Axis while the bones remain the same. Again, I'm a beginner and know only a bit of what most experts know about these issues. What I can say however is that I made changes to the model before parenting with automatic weights. All the vertices in the model were disconnected, so I connected them all individually. I thought it would save some time if I deleted half the model (without deleting the bones) and used a Mirror modifier to speed up the process. This is the first time I've ever posted to this site so please bear with me. I've searched long and hard for an answer to this problem and have come up with nothing so I thought I'd ask the question myself in hopes that I get the answer.
In edit mode select all vertices, then press delete doubles in the tool panel (shortcut T). Then, in object mode, apply your mirror modifier, then apply rotation and scale of your model (ctrl A).
Then try parenting with automatic weights; if failing, you will have to weight it by hand, i.e. with the weight painting function.