Kinda just unfortunate people leave a well open for that long, its fine if it is just you, but aquifers feed to many other people. That sort of thing is what leads to very, very tight regulations on wells and extra costs and so forth, when people don't care about others and mess in their water..... Sorry for the soap box, more of a general musing , not meant to aim right at you..... I will guess then that your temporary setup will look about the same 3 years from now, I'm kinda a temp setup get around to it later (not!) myself so I understand that part......
I always thought it was best to keep 10 feet above the bottom of the well, if you get down to the bottom under 5 feet like you are the pump swirl always kicks up the bottom and always creates the clay swirl. You said this was a very high output well, why go so close to the bottom?
6-700 gallons is nothing, my much deeper but smaller well has pumped more than that out in the past 2 hours, on its way to filling the 2500 gallon cistern I fill every 4 days.
You need to run a lot more water, full bore (I understand back pressure and such, but just running strong), to flush the system out. You aren't even broken in yet at all.