Interesting, and potentially, very sappy waffy.
As with all time travel stories, one has to accept the conditions and not get all tangled up in the 'but why not take her to such and such a time, or go back before this or that happens'. The time travel is just a vehicle to put the characters into the situation you want them to be in. If you over analyse it, you can always punch holes in the logic, because time travel, after all, is illogical.
Now, as to the story. I can accept Lois being strong enough to take in all the incredible things she's hearing. After all she is probably still experiencing a certain level of shock. Also, taking in so much unbelievable stuff, it's often easier to just numb yourself to it and accept it.
We don't know her past, so we don't know how much she has been 'hurt' by men in the past so we can't be sure of where her defenses might be. Given that, though, she doesn't have the initial competitive anger toward Clark that the other Lois had, and the addition of the super hero to keep her from recognising the real Clark earlier. The fact that she was able to fairly quickly become friends with Clark still given all that says that Lois did recognise some things in Clark earlier. So it is possible for the 'bond' to come through a little easier for altLois since she's alone, vulnerable, and doesn't have a lot of baggage to deal with.
The BIG problem is going to be Clark's explanation of his obsession with her. How is he going to skirt around the issue so as not to frighten her, or turn her off. The built in 'I'm just a substitute for the Lois you really love' bit is a hard one to overcome. (And not one likely to be conquered in one more instalment). I'm curious as to how you, the writer, are going to skate by that one.
I've caught up with reading this now, so you can post the next part.
Tank (who was missing in action yesterday due to a bad day at work which then made him almost late for band practice, which then made it late by the time he got home, which then made it impratical to go online)