The VG Resource

I am currently preparing 3D and Live2D models from Toaru Majutsu no Index: Imaginary Fest. Many of the characters with Japanese names have both a given name and a surname. Does this site have a preferred order for these names?

Some of the characters have sprites/models from other games on here already. One has "Mikoto" as her given name and "Misaka" as her surname. Most of her entries on The Spriters Resource have it as "Mikoto Misaka" (given name first), but a couple have it as "Misaka Mikoto" (surname first). This makes it seem like we prefer the Western name order over the original Japanese name order, but I don't know if it's actually indicative of what is considered best practice here.

I don't believe there's a preference here. It all depends on how the submitter writes the name.

^ Pretty much that. Though we tend to lean more towards Western ordering for character names, it's not exactly something that's mandatory for submissions. That being said, you're more than welcome to submit revisions for the names to make them consistent across the site.

Personally, I'm using forename surename (western variant), since this is an English-speaking site and easier for people to understand.
But of course you can also use the JPN version, if it is a preference of yours.

Usually I just go with how the game itself puts it because some have done it both ways like King of Fighters where the Japanese Mai Shiranui has her surname last but Korean Kim Kaphwan has surname first.