1) "Did you quit your job in the weekend?"
"I was thinking of doing so for a long time, but then I decided not to".
2) "Did you quit your job in the weekend?"
"I had been thinking of doing so for a long time, but then I decided not to".
Are both the past continuous and the past perfect continuous possible in this sort of sentence? Does the meaning of the sentence change according to these two different kinds of past?
Did you quit your job at the weekend?
I had been thinking about it for a long time but I have decided not to.
I don't think the meaning of your two sentences are substantially different but they don't sound completely natural. Of the two, I prefer the second but I would word it as I have above.
I took these sentences from a MacMillan book for the Cambridge CAE...I did not write them actually...I have just reported them here because I had some doubts about the two tenses I wrote above.
Please let us know if you are quoting from somewhere.
Macmillan/Cambridge or not, I agree with emsr2d2 about replacing in with at. I don't find the original sentences particularly unnatural, but they appear slightly more formal; I would probably use emsr2d2's words in conversation.