My problem is, in What Remains, Jim tells Elisabeth that Reynolds is "coming a' courtin'," and Reynolds does come to their house for a date. However, it is in the next episode, Runaway, that Reynolds asks Jim and Maddy both if he may court her, and explains to Maddy that he is supposed to address her in a certain way, then speak with her father, then call at her house. So the fact that he "called at her house" before talking to Jim, and apparently Jim knew he was courting Maddy (and what's more, Jim calls it courting even though it's an antiquated practice), before Reynolds actually asked Jim... doesn't make sense. So it seems to me that the airing order should have been Instinct, then The Runaway, then What Remains, etc.
Here is what I've been able to figure out, as far as specific plotline continuity:
The box: It makes its appearance in Runaway, and there is no mention of it in What Remains.
Boylin/Josh's deal with the sixers: Skye tells Josh about Boylin in What Remains, but there is no mention of Boylin or Josh and the sixers in Runaway.
The only thing I found out of order with Runaway before What Remains, is Zoe's dinosaurs. At the end of What Remains, Jim goes into Zoe's room and asks her what she's got, and she shows him her dinosaurs. Then Elisabeth comes in, and Jim says, "Look what Z made." But in Runaway, Jim tells Lea that Zoe makes them in her spare time. But, I figure this is small potatoes compared to the rest of the plotlines, and it could be that when Jim asks Zoe what she was playing with, he was just talking to Zoe as though he's, well, talking to a six year old.
I also initially thought Bylaw was maybe supposed to be before both of these episodes (that What Remains and Bylaw were switched, with Runaway staying in the middle). It's in Bylaw that Jim brings Zoe to Elisabeth's work, when Zoe had pretended to be sick in order to come home from school. Jim: "Somebody has an earache." Elisabeth: "And yesterday it was your tummy, wasn't it?" But in What Remains, Maddy brings Zoe to the infirmary saying, "Zoe's sick. And this time she's not pretending." Before What Remains, we did not see Zoe pretending to be sick, just showing her general strong attachment to her mother. Also, there is no mention of Maddy/Reynolds in Bylaw. But, I ruled out Bylaw being before What Remains, because Boylin tells Josh that Mira wants to meet with him, so this is obviously after Skye tells him she "knows a guy," which was in the beginning of What Remains.