1. What do you mean by that?

2. What do you mean by saying that?
(Does #1 mean #2?)

3. What do you mean by "TGIF"?
4. What do you mean by saying "TGIF"?
(Is #3 from #4? Is 'saying' deleted before "TGIF"?)

5. This room is for VIPs only.
6. This room is for only VIPs.
(Which one is right? Are both OK? Which one is commonly used?)

7. He read this book in a day.
(What does 'in' mean here? Does 'in' mean 'within' or 'after'?)

1 - 6 are all OK, but including "saying" in 2 an 4 is a bit awkward.

7 - "in" means "within."