Whenever I use the WMMT SMD importer to import an SMD file, I get this:
"--Runtime error: Bone index out of range:0"
Will this affect my custom modeling in any way?
I'm not really sure about that. I've never seen this problem. My assumption is that the SMD is incomplete or incorrect. To find out how well it then re-exports is going to be a matter of testing it and seeing if it works.
My guess is that the Skin modifier will need to be modified/fixed after import.