There is no reason for BD to cover up for a boyfriend if he killed her daughter. Suggesting something like that is getting way out there IMO.
There is no reason for him to turn in the overalls if they were contaminated with evidence. It would have been much more likely that they would have been destroyed somewhere if that were the case.
The separate trips would have required that the friend be asked for a lift well prior to them actually leaving, so BD wasn't "waiting" for anyone. It is reasonable to think that SA had been called in early (perhaps this was the final straw that led him to just say to hell with it and quit), and BD called a friend to ask for a lift to work. The call would have had to be made some time prior to departure so that both of them could be sure of getting to work, and there must be phone records to back that up.
SA went to his GM's house. The "pings" between 6:35 and 6:56 would have been phone calls he made when he got there and found no one there. That is around the time BD would have been passing by, which explains why she did not see him. My guess is that the phone calls would have been to residents of the house, initially, then probably to his mothers house as he adjusted his plans to go there instead.
The amount of time is less than 2.5 hours, because the "pings" are actual phone calls. There would have to be time after and before the two sets, plus there would have to be time to load the body without being seen, drive out to the lake, dispose of the body some distance away, then drive to Big Spring. So that does not actually leave that much time.
Also, there were very likely people at the mothers house, and he probably has witnesses verifying that he was there earlier than the first phone call there. We don't have any information on that, but my guess is that is a big reason why the investigation petered out - they ended up with a situation where SA's movements were unambiguous and corroborated. Once that happened then they could not in good faith get additional warrants citing that as probable cause.
BD didn't get the cell phone from HD because it was the house phone. It would still have been in the house after HD left, so nothing odd about that. BD called DD from work the next day. If it was the house phone then it must still have been in the house for DD to answer it, so obviously she did not take it with her that day and used her phone at work to call DD to tell HD to come home. Incidentally, she could not phone CD because he supposedly did not have a phone and therefore she had to send DD over to see if HD was there. BUT, in the account coming from the other side (the paternal GM IIRC), CD had called his mother to take the girlfriend shopping that afternoon (which leaves CD's activities uncorroborated during the period HD supposedly went missing) since he didn't have a car (don't buy that). So he DID have a phone. That implies that the level of communication between BD and CD was probably less than cordial. Either that, or one or both are lying.
You might also ask why she didn't call MB's mother to ask as well. Obviously there was some sort of drama going on if HD had taken off to overnight with MB apparently without BD's knowledge, and she did nothing about it that night, but the following morning she was concerned enough to call DD to go fetch HD. That tells me two things: (A) BD and MB's mother were not even close to being on talking terms, something that has been clearly evident subsequently due to the passive-aggressive hostility the two showed towards each other when talking about it in interviews.; and (B) there was something going on with HD that the family were very concerned about. If there was not, BD would not have suddenly got a bee in her bonnet about HD when she got to work the next day.
She may well have called SA to take her home, and discovered then that he was in fact in Big Spring.
If I were the investigators I would pull the phone records for all of the following phones:
SA's phone (obviously they have done that)
BD's cell phone (they had a warrant to do that, but we have not heard any results stemming from that)
BD's work phone
SA's work phone (such as it might be)
CD's phone (and any other phone in the household)
Any phone DD and/or his friend reasonably had access to during the afternoon through to the morning
Any phone MB had access to, particularly any cell phone
Any facebook accounts or other social media any of the above had access to
The main thing to look at would be to see who these people called or were called by, in order to build a general framework of what these individuals were doing and where they were doing it during the period extending from the day before HD disappeared to the day after, so a 72 hour window.
I would also be curious as to the reasons why SA believed that HD was in Scurry county, and why CD believed that she was in various towns to the south. When the dogs tracked to the hotel, CD wanted to view the surveillance tapes, and the only reason IMO for doing that he expected to see a known face among that footage. My interpretation is that both of these guys thought that she was with someone but wouldn't say who. Remember, CD was pretty ambivalent about SA being accused, which is hard to imagine if he seriously thought SA harmed a daughter he was apparently so committed about. So IMO that means that CD knows that SA isn't the guilty one.
I'm telling you, there is something else going on here.