Glad you found a solution! I'm still, unfortunately, hung up on other projects and won't have the time anytime soon to make improvements. I hope to find the time next year though, as there are several things I'd love to add on top of the bug fixes and other QoL changes.
No worries - I appreciate the extra work that something like this requires to support :)
Putting this here for next year - the thumbnail error in the LTS version - seemed to be caused by GMLink being unable to find the yyp file within each individual sprite (file structure issue I assume, as you mentioned above).