This is ugly stuff!
1) He has been reading this book in the last two days. (I think it doesn't mean )
This IS ok but I think that "---during the last 2 days." would be slightly more elegant although I would be perfectly happy with:
"In the last two days he has been reading this book."
which seems, to me, a more natural phrasing.
2) He has been reading this book for the last two days.
Well, y-e-s - although I'm not entirely sure that I agree with WS2's comment:
Means that he has been reading the book (not necessarily continuously) for the last two days.
and finally we come to:
3) He has been reading this book for three times in the last two days.
Again this is the actual construction of the sentence:
"Three times, in the last two days, he has been reading this book"
would be fine.
Some people say IN shouldn't be used with PPC others say it's OK.
I am sure that the purists are correct, but stuff 'em, as long as you can make it look good & read well. It's OK.
Hope this helps