Virginia,
Via PM Morgana and I were discussing(debating) the validity of Jor-El being alive and the planet Krypton not exploding and hence how did Kryptonite get to earth without Clark's ship to suck it along at light speed when she mentioned this being an alternate universe story and that timelines from the series don't have to match up with the story in an AU story.
As for the other questions, some may be explained by the above but the character Dr Pete Ross, his knowledge of Clark's secret, and his penchant for doing favors for his old Smallville buddy Clark showed up in Morgana's "Stranger in Our Midst" when Clark pulls him in to tend to Lois's bullet wound in the arm without reporting it to the authorities. Fortunately I just finished the past weekend so I did not have to dig and dig to figure out where I had seen this before. His and Clark's backstory is fleshed out a bit more in that story.
Mike
