Time to go down another Radio Rabbit Hole! - thanks to archives that I subscribe to that have a complete set of issues of the Des Moines Register. What follows is a summary.
The formation of Iowa Public Radio dates to 2004, with an executive director being chosen in 2005. She was Cindy Browne, who had worked in public broadcasting in Minnesota. She had to resign in 2008 due to health issues, and she passed away that year. Even with health issues, she was able to consolidate station schedules beginning January 1, 2007. Further consolidation occurred the next couple of years. This was somewhat controversial. Listeners to the individual stations were upset that some of their favorite programs (including one that resembled Prairie Home Companion) would be shifting time or would go off the air altogether. There was also the complication that WSUI/KSUI and WOI each had their own public-affairs program titled The Talk of Iowa. The biggest controversy, though, was over The Diane Rehm Show, which was scheduled to air weekday mornings, repeating weekday evenings. "Nearly 750 complaints" were received, especially from fans of On Point, which KUNI in Cedar Falls had been airing in that time slot. On Point then replaced Diane Rehm in the morning slot, but not the evenings starting the third week of January 2007. (I told you this was a rabbit hole.)
It's unclear when there was a split between the classical and news networks. The classical network, at least in the Des Moines area, is served by rimshots surrounding the city, and seems to be a secondary network to News/Studio One. Moreover, the decision to split one FM network's time between news and "Studio One" isn't described. Most of the stations in the network already existed in 2007. "Studio One" was a concept that came from KUNI, which had been airing a full-time eclectic/AAA format. That format ceased in 2007, but remnants were still on the schedule, and by 2008, there were newspaper ads describing the network as "News and Studio One," as it remains today.
The licenses were retained by the state universities, under the supervision of the Iowa Board of Regents which governed all three, because they were still providing financial support to the network. There was a goal established to phase out this support by 2016, then by 2017...and finally the phase-out happened last year, at which point the Regents voted to transfer the licenses to IPR.
One thing that surprised me was that the Ottumwa stations were originally put on the air by Iowa State University, not the University of Iowa. (This part of the story comes from Ottumwa Courier archives.) This was the outcome of a 10-year-long campaign by the Wapello County Board of Supervisors to improve public radio coverage in the Ottumwa area. Federal grants finally came through in 2005 and the Ottumwa Courier reported that the stations (one for each network) came on the air in 2007. There were also competing applications that had to be dealt with. The Courier carried complete minutes of the board of supervisors meeting (required to be published in a newspaper of general circulation under Iowa law), and the topic - and impatience with FCC procedures - came up frequently in those minutes, as well as in Courier editorials.
Yet, even with these origins, the Ottumwa stations' IDs don't appear with the IDs for the central Iowa stations. Finally: an excuse to re-visit Ottumwa! - to see where those IDs are coming from. I suspect I can't get those stations well, if at all, in Centerville, which I re-visited last year for the first time in 50 years.
The network appears to be partitioned between central and eastern Iowa but I still believe programming and operations are based in Des Moines. There may be a few specific programs produced at Ames, Cedar Falls, and Iowa City, but all indications are that programming is centralized in Des Moines.
Another thing to note is that the FM stations in this network cover only the eastern 2/3 of Iowa, mostly. The public radio stations in Sioux City (repeater in Okoboji) and Council Bluffs have had no interest in joining the network. KWIT in Sioux City is owned and operated by a technical college and still runs a news/classical/jazz/blues/AAA format; KIWR in Council Bluffs runs what amounts to an alternative-rock format. IPR's AM stations still can cover most of these areas; Council Bluffs can also get NPR programming from KIOS in Omaha.