Well, so far in my re-read I have to say things flow.
I also have to admit I totally forgot that Lois saw Superman's ship in the B39 warehouse, and did not figure out that it worked as his ship because he had been smaller then.
I did come across a typo in this section that just grated.
“Wrong?” he echoed.
He had no idea what she talking about. From his point of view this was anything but wrong.
I am pretty sure that should be "He had no idea what she was talking about."