Franconia (as a whole)

Section 1. Outside the NewUS but inside the CPE:

Brandenburg-Ansbach (Lutheran)
(At the partition of 1541, 689 square miles; about 110,000 people)

Brandenburg-Kulmbach-Bayreuth (Lutheran)
(At the partition of 1541, about 660 square miles; about 80,000 people)

Nuernberg (Lutheran, about 40,000 in 1600)
Just before the outbreak of the 30 Years War, the population of Nuremberg reached its peak (50.000). See:

Section 2. Inside the NewUS:

Diocese of Wuerzburg (90 square miles; Catholic)
city population about 6,600 before 1500; Hochstift as a whole had about 170,000)

Diocese of Bamberg (65 square miles, Catholic)
I haven’t found a population figure for the city about 100,000 people in the Hochstift

Exclave possessions of the Archdiocese of Mainz (Catholic)
Aschaffenburg (this was an important city; in 1648 OTL, the mayor of Aschaffenburg, in his capacity as Chancellor of the Electorate of Mainz, was the first signatory to the Peace of Westphalia)

Section 3. Not sure:

County of Hohenlohe (about 60,000 people)
Divided as of 1632 among three lines of counts, partly Catholic and partly Protestant

Other Franconian Imperial Cities (I should be able to get population estimates from the Deutsches Staedtebuch, but haven’t considered it worthwhile. Figure that all were significantly under 10,000)
Rothenburg ob Tauber, 6000

Hundreds of Reichsritterschaften and tiny principalities (population not statistically significant).