well after she find out that the naru in her dreams was actualy the brother he was looking for
she was quit confued shocked and noticed that she did loved his brother who was dead
its somehow sad that she will never be abel to be with him and that she only got to know him because he was dead...

but the question is

did she just love him or does she love naru now
i didnt quite get it in the end...

I think she didn't really love only one or the other because she though they were the same person. She loved them both together as one. However now that she knows Gene is dead, she will probably eventually get over him and love only Naru. You can't say she loved only Gene because she really spent more time with the real Naru and was still in love with him.

http://lkk.livejournal.com/189335.html?page=3&cut_expand=1#cutid1

Someone has posted a summary of the original novels of Ghost Hunt. If you read the last bit and the comments of the poster of the essay (who has evidently done some thorough and trustable research), you find that

the author intends for the canon couple to be Mei/Naru but that she doesn't like writing romance and she doesn't plan on writing any more for the story.