Ĝan Ŭesli Starling
Member
...my research indicates it mostly becomes introduced to a well when work is done like if the pump is replaced or some other maintenance, or if the well isn't sealed with a good cap.
Other kinds of bacteria, yes. Iron oxidizing bacteria from the surface, for instance. Iron and sulfate reducing bacteria, however (at least according to every source I've so far read) are reported as naturally occurring in most ground water to at least some degree. Requiring neither air nor light, but only moderate temperatures plus sufficient iron or sulfate to maintain their metabolisms, they are near omnipresent.
As a career test engineer with much experience of various other kinds of pumps, may I propose a hypothesis? Your pump which needed replacing, prior to its final demise, had been for some time operating with much reduced efficiency.
As such, it had likely been running warm. Its waste heat warmed the water inside your well sufficiently for the naturally occurring (and still present) bacteria to bloom and thrive. Like how algae blooms in lakes during summer. A few scant extra degrees may have been all they'd have needed. Shock treatment wiped out the established colony; and now your brand new, efficiently running pump leaves them sluggish for being chill.
It is for this same reason that untreated water from my own well runs clear from the tap, then upon being allowed warmth and air, slowly develops an orange tinge.