Do i have to do all the halloween storyline quests during the halloween event?
I'm of the understanding that the "Ghost in the Machine..." quest is THE Halloween storyline, and that will be done away with at the end of the event. The side quests are associated with the individual building/item, and will remain. I could be wrong, but that's how I understand it to be.
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Take care of all the Halloween events first. That wii end. The other quest can wait
Somewhat terrible idea. You will want to do the side quests, at least after or during the main story line. I'm nearly through the main story line and it's only been a week. I anticipate it to finish this week as the quest times diminish.
However, if you put homer on his 12 hour task when he's not used, you get like 5 Goo. If you have him eat the pumpkin house (1 time quest), he will get 25 Goo when the task completes. So if you wait that one out you'd have loss that 25 Goo for the quest completion.
I found it best to put Homer on that quest when Apu, Ned, (Frink if you have him) trigger their 24 hour quest (part 7 I think). So all 4 were on Goo earning quests. Once Homer was done at the same time he was ready to trigger the next part 8 or whatever.
Basically you will want to complete any of the Halloween tasks. If Lisa is not used in the story, take 2 hours out to complete the Burial Grounds. You'll get 50 Goo for that (in addition to the cool new ghosts). She can re-sync with the other Trick-or-Treaters easily.
Any side quests you'll eventually want to do when the character is not part of the main story line. After they are done in the story line complete their side quests. After that, then go back to the Goo earning task (for Homer/Lisa). You should have plenty of time to get the side stuff done and the main story as the main story is only 15 parts.