I'll start with noting that this wasn't the originally planned Part 2 of this series, but that I realized that I had another thing to define before getting into the nitty gritty. So, we've got this one, about the subdivisions of the divisions I've made.
Eras are big overarching stretches of the strip marked by common creative threads. (Even if, in the case of the Transition Era, those threads consist of 'being stuck between two clearly delineated eras' and 'watching Muir struggle to figure out what he wanted to do with the strip'.) But within the eras, there are similar divisions, story threads taken up then abandoned, style choices that come and go, obsessions and oddities that appear, then disappear. Taking a hint from geologists, these will be called periods.
Now, I expect that the future Eras are going to be quite involved, but the Mystery Business(tm) Era is a simpler beast--it divides cleanly into the Early Mystery Business(tm) Period, 2002 to 2004, and the Late Mystery Business(tm) Period, 2005 to 2007. The Early Period is both formative, and also, clearly something Muir is doing as a hobby. Both 2003 and 2004 see him take lengthy hiatuses, and even in 2002, where the strip is active for only two months, he still manages to miss a day.
The Late Period, however, marks the brief apogee of Muir's mainstream involvement. From 2005 to late in 2007, Day by Day was actually syndicated in a handful of newspapers. This saw Muir attempting a more rigorous, professional attempt to produce strips on time, and also saw some developments in the characters and politics of the strip, which will be gone into later. This syndication ended abruptly--likely of self-inflicted wounds on Muir's part--and so by the end of the Late Period, Muir was transitioning the strip back to online only.
And this brings up something connected to all this that has to be mentioned--the Mystery Business(tm) Era is the shortest by a significant margin. The only one that is presently shorter is the Gunpowder Era, and that is presently ongoing, and should outstep it during the course of this year. The Compound and Transition Eras outpace it by a year and multiple months, and even that undersells its brevity, because again, there are significant hiatuses in the Early Period comics. The foundational era of Day by Day has the least strips. I suspect there's something to this, and yes, I will go into it in the near future.