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I'm using a propriety markup language with character entities similar to HTML, with & as char. start and ; as the end, but instead of, say, ldquo it's just ld. Regardless of what I do with the document classes or syntax files, TextPad will only display the "character" color on the entities that are the same as HTML ones. Is there any way to apply the character color to non-HTML character entities?

You need to create a new document class. This is not really scary as you take, for instance, the html.syn syntax file in TextPad/system directory and copy it with a new name to your textPad/user directory.
This file should then be editted to suit your markup language.
Finally select Configure/New Document Class from the TextPad menu to activate this syntax file.