Kurogane and Tomoyo are supposed to be together just like S+S!!! It can be seen that kurogane pines to go back to his world so that he could be with her again. And though he often call her '*****', it is because of his personalilty. And everytime Kurogane sees another Tomoyo in another world he would absent-mindly call her Tomoyo-hime, though knowing that she would not be the Tomoyo he knows. This shows how much he misses her.
As for Fay and Chii.. well she's his pet. He prefered to have her asleep than to suffer the annoy of waiting for him to return as he is not even sure that he would. He tried his best to make Chii happy in the anime when he met her in one of the worlds. For Fay and Chii, the relationship is not that obvious but there is a subtle hints here and there that he has a thing for her.
I don't think so...I mean...Tomoyo in Piffle was completely obsessed with Sakura -- just like she was in CCS. It would be a really weird change of her personality to have her going from liking girls like Sakura in CCS, to suddenly liking guys who are angry, tall, and grumpy 90% of the time. I've never seen anything to imply that Kurogane and Tomoyo are 'meant to be'...I mean. Tomoyo's like a mini-version of Kurogane's mother. XD
And FaiXChii? I once again point out Hideki. Clamp don't break up their canon pairings -- and Hideki and Chi were canon in Chobits. It would make a lot of existing fangirls angry if they broke up HidekiXChi...which I don't think they will seeing as Chi spent eight volumes of manga searching for her 'someone just for her' (Hideki.). It would make Chobits see pointless if she just got paired with Fai.
...But whatever. XD It's up to you who you like. Those are just my opinions. Personally? I'm enjoying watching Kurogane and Fai's relationship grow. They're so funny. And have some serious dynamics. Heck, I think I'm only really reading Tsubasa because I enjoying watching them interact. XD;