When importing from one file to another is there anyway to sort or specify the left side (source file) field order?

I know it is possible to sort the right side (destination file) field order by name, field type, matching names, etc. But trying to find the field name in the source file can sometime be a tedious task, especially when there are hundreds of fields.

I don't know if this is a limitation that pertains to version 6 or if FM has fixed this in later versions?

Nope, can't move 'em. The current FileMaker file doesn't really have control of that other file.

In latter versions of FileMaker you can change the receiving table in that dialog. But you can't do anything to the file you're importing.

The best solution, in my opinion, is to get hold of the source, and rename as many of the fields as possible to be exactly the same as your target table (file in your case). Then you can use Matching Names for most of the heavy lifting. You still have to check though, easy to miss one.