You obviously have given everything careful and serious thought, and that's commendable. Here are some more things for you to think about.
1 - Why to fill in the chimneys , practice that would work against Peraltas like would work against the " jump in " peons . In that era like today , the time was money .
My thinking is that Miguel had reasoned that it would just take him and his hundred strong crew of peons to cover/uncover in one or two days, that a handful of men would have had to take a good couple of weeks, or even a month to uncover. That in itself would discourage just about every peon from attempting to go back.
I disagree that they operated on a "time was money" for philosophy- I believe it was more that they had to make every trip really count, because it was a dangerous journey of over 300 miles, one way. With such a large caravan, it would no doubt have taken around a month to travel up there, and another month back. With that in mind, it's not hard to envision them staying up there all winter, and everything I have read and seen in those mountains, myself, points to that. Another benefit in doing that is that by staying there up all winter, it forces anyone else to have to come back in the inhospitable summer months if they wanted to work behind Miguel's back.
2 - Why to leave around rich in gold ore tailings , that would born suspicions and would start an attempt to discover the source of those tailings , when they could threw the useless tailings afar in a place that would been hard to be discovered and if discovered to be not easy to recognize from what type of diggings the tailings were produced .
It's absolutely impossible to cover up the footsteps that a hundred plus men and twice that number in burros/horses were going to leave up in the mountains. (Think about the number of ironwood trees that were cut down to continuously feed a smelter). If you're going to dump the tailings in one place, even if it's far away, you're still going to leave a well-worn path back to where the tailings came from. Even if you dump it in three different places, you're going to leave three paths that eventually converge. Don't forget that these were the days of the very skillful trackers.
So my reasoning is that instead of working against that, Miguel turned it to his advantage by scattering the tailings all over and leaving a myriad of paths. I believe that Deering mentioned this "myriad of paths" in his account (correct me if I'm wrong).
Also , in none account to this day was stated how rich in ore tailings were found around or have led anyone in that area . What John Reed stated about the rich tailings near the shaft/placer mine ( the shaft is few feet from the dry wash bottom ) , were the tailings left by the Mexicans ( maybe Peraltas ex peons or ex peons relatives ) who worked the mine at the time when John Reed and his father were there , and at the time Waltz found the mine . Those last Mexicans who worked the shaft in Waltz era , didn't bother to hide the mine or the tailings , like the clue says : " From over the top of a low ridge you could see down the far side where there was a small clearing, an open hole and a mine dump. (Herman Petrasch) " .
I believe Reed's trip was in 1884, if I'm not wrong, so that would be some 40-odd years later. And you are probably right, what his father stumbled on was the result of someone going back many years later, or someone who had stumbled across one of the chimney deposits left open as a result of the massacre which "froze" an ongoing operation. That is, if the Reed account is truthful. Don't forget that Bark eventually became disgusted with Reed.
And if Peraltas have heard about the Superstitions Mountains to have rich mines and other stuff , and how that info led them there , i believe is truth . But I don't believe they knew the exact spot of that location from the beginning .. To find it , they have started prospecting from the Salt River into the mountains , and after many years , they were able to discover the old diggings , but not all at all . The fact how Peraltas named the remains of the Santa Fe church as Caverna con Casa and Casa Caverna , this make me think how they didn't know what the ruins represented and how didn't find what they were looking for and what would been the reason of their quest ( if this was ).
This part of the tale is perhaps the most interesting to me- as I mentioned, Miguel was led up there. He didn't just go 300 miles on a whim or to look around for old diggings.
Also the trail they took led them to Twin Buttes, which meant that they followed.... a very old trail.
