I really think it may have been during the 40-minute gap in NC. Otherwise, he had to drive over an hour from NC back to Farmington in a (likely) unreliable, unfamiliar truck with a dead body somewhere in it. There's so many variables and what-ifs that could've happened on that drive back. I'm just not convinced he would've taken that risk.
Also, this was planned. He knew what he planned on doing with the body. 40 minutes is a long time to move some things from car A to car B, especially when you've already spent longer than you probably originally anticipated cleaning blood in a garage.
The one thing I can't figure out is the phone. The warrants make it seem like JFD's phone got to Lapham, stayed at Lapham, then was disconnected 40 minutes later. If that IS what happened (and LE aren't just purposefully leaving info only the killer would know out of the warrants), it doesn't make sense to me. He brought her car and phone to Lapham, left to dispose of the body, then swung back around to power off her phone? That seems foolishly dangerous and unnecessary.