1. Your trying to make a coherent timeline from Scooby-Doo? Brave, brave man, far braver then me. If your insistent on it, i can tell u that most people dont consider anything with Scrappy or real ghosts in it in continuity. Scrappy is basically a personal preference, and shows with real ghosts and monsters (like "13 Ghosts of Scooby-Doo" and the 80's DTV's) kinda violate the spirit of the original series. The exception would probably be the 90's DTV, where the ghosts and monsters were considered the exceptions and not the rules. Also, "A Pup Named Scooby-Doo" is probably also questionable as to continuity, again due to peoples personal preference. If that helps u out i dont know.
2. My guess is that its because Frank Welker is a full time voice artist, thus available to do the movies, while Casey Kasem isnt, thus he was doing something else (what that would be i have no idea) and wasnt available.