ahk is a good general purpose windows solution.. though for heavy text manipulation, perl wouldn't be a bad idea either (as much as i hate perl).
now this jumps out at me:
What's more, I don't believe Clipboard Help+Spell's default mechanism of exchanging information with a custom script by passing the custom script an input and output file is going to work here... unless perhaps the script is called multiple times for each word parsed from the current clipboard entry. Because... I don't believe there's any way to tell Clipboard Help+Spell that the output file contents aren't supposed to all be all one clipboard entry? So, I decided it'd probably be best to have the script itself read the current clipboard entry and, of course, paste back separate clipboard entries for each word parsed from the current clipboard entry.
that's an interesting dilemma.
you are right that CHS is going to take whatever you output and make it as one clip.
your proposed workaround, of having your tool send multiple clips to the clipboard directly may not work.. that's because CHS probably (i dont exactly remember) disables clipboard monitoring while it runs a clip processing script.
now what i CAN do is put in place a way for the output format to specify multiple clips -- like by using an agreed upon separator like "@@@@CHS:NEWCLIP@@@@" and have CHS auto separate clips into multiple clips when processing.