Today's Democrat and Republican parties seem quite simple in understanding them. With Democrats ranging from progressives like Bernie to moderate-right (like 90s Clinton and establishment Dems) and Republicans ranging from moderate-right to far-right and clustered really around cultural and social-welfare/business as deciding factors.
We all know how the Civil Rights movement/Goldwater/Southern Strategy reorganized the parties around modern "conservative/liberal" ideologies, but I am having a hard time understanding (despite falling in to a wiki hole) how the two-party system operated between the time of post-Lincoln Republicans to the Kennedy-Johnson-Nixon era (1890-1950)?
How did people even pick their parties? There seems to be some ethnography to it with Catholics going to Democrats and Protestants going to Democrats? But the parties had a WIDE range within each party when it comes to progressive vs conservative, pro-corporation vs pro-worker, isolationist vs interventionist.
There were progressive Republicans (like Teddy Roosevelt) and Democrats (FDR) at the same time. I see a lot of discussion about Democrats protecting the Southern Jim Crow era (the Solid South), but how does Truman become the nominee and Civil Rights end up on his platform with all the Dems in the South?
Republicans were often progressive, but they were also puritanical with the prohibition on drinking.
The New Deal got Blacks to support Dems.
Trying to understand what actually defined these parties if anything at all.
Was it cultural (Catholics vs epiestical Protestants vs Evangelicals?)?
Was it purely economic (pro-tariffs vs anti tariffs, farmer vs industrial business, Unions/Anti-Trust vs Corporate Business)?
Was it isolationist vs internationalists?
Is there a politcal theory component I am missing? (Central vs Decentralized governance)
Maybe this is why bipartisan politics was much more active back then since both parties had the full spectrum.
The problem is that you are really looking at a very long period in American history going roughly from 1876 (end of reconstruction) to 1964 (First Republican to win the southern states). During the time of which both the Republican and Democratic parties changed greatly.
The issues you identify are basically correct, but does not apply uniformly across the era you are referring to. Nor do they apply uniformly through either of the two major parties. Unlike America since roughly the Bill Clinton era, in which both parties have acquire a great deal of ideology comformity at the national level. Parties of the late 19th/early 20th century were true big tent coalition: in which groups greatly seperated from each other voted for the same party at the national level despite ideological differences and party infighting.
A good example of this is monetary policy: in 1896 William Jenning Bryan wins the Democratic nomination as a "Free Silver" Democrat, but he is opposed by the "Bourbon Gold Democrats" from within his own party, but is also supported by some "Silver Republicans" across the asile.
How did people even pick their parties?
A mixture of issues of the day, patronage/party machines, and flat-out racial/religious identity politics in some regions.
There were progressive Republicans (like Teddy Roosevelt) and Democrats (FDR) at the same time. I see a lot of discussion about Democrats protecting the Southern Jim Crow era (the Solid South), but how does Truman become the nominee and Civil Rights end up on his platform with all the Dems in the South?
In the 1900s there was a progressive wing of both parties, the progressive wing of the Republican party lost the intra-party struggle (culmulating in TR's third party run in 1912).
Progressivism does not mean the same thing it does today: back then Progressivism contained a lot of racist ideas such as social darwinism or eugenics, and Theodore Rooservelt himself vented against "hyphenated Americans". President Woodrew Wilson, a progressive who instituted anti-Trust action (Clayton act of 1914) and the federal reserve, was also deeply racist. Having racist views was part of being a progressive in the early 1900s.
Was it cultural (Catholics vs epiestical Protestants vs Evangelicals?)?
In the north, yes, Catholic immigrants living in big cities was a vital Democratic constituency, while Protestants were a Republican one. In the south all whites almost uniformly voted Democratic post-reconstruction.
Was it isolationist vs internationalists?
There were wings of both parties for and against foreign intervention (see TR vs Harding)
but how does Truman become the nominee and Civil Rights end up on his platform with all the Dems in the South?
Northern Democrats were strong enough in 1948 to put civil rights in the Democratic platform despite southern opposition at the National Democratic Convention.
In response southern Democrats walked out of Democratic party and rallied around third (fourth) party candidate Strom Thurmond, but the New Deal Democrats were such a commanding majority in 1948 that they are able to win a national election even with a significant party of their coalition splintering.