So the manga's storyline is different from the light novel and anime? How so?

Does Ryuuji end up with with a different girl than the one he was with in the novel?

That...I don't know. What I do know is the recent episodes of the anime will now base on the novels. Since the last volume (Volume 10) will be release this coming March, the author will now have a cooperate discussion for the anime ending of toradora.