I don't know anything about flukes, but I went through some similar stuff with a hound doggie who contracted tick disease (ehrlichiosis with babesiosis conifection). Lots of liver complications

and strange stuff coming up, including some bright yellow poop which is characteristic of a hemolytic anemia they get and lots of very strange vomiting.
I've heard liver cancers can cause some pretty strange things, too.
If your cat had a certain kind of upper respiratory infection, too, that's bad.
It was likely NOT the shots which killed your kitty, in any case --- it seems more likely there was some kind of serious underlying condition which was complicated by the shots.
I've HEARD cats can develop pretty bad liver problems if they go too long without eating, too. If your kitty was dehydrated and jaundiced, it may have occurred due to inadequate food intake.

In any case, I am really sorry.