Well to start I'd just like to point out that Virginia, Maryland, and Texas (Southern states by virtue of their shared history with slavery and location below the Mason-Dixon Line) each have a GDP per capita higher than the US state average. Maryland and Virginia are also in the top ten for median income and percentage of residents with higher education degrees, and in the top eleven according to Human Development Index. However these states are the exceptions for their region: the Chesapeake states have increased in wealth over the past century thanks primarily to the expansion of Federal Government while Texas has been thriving off of energy. The rest of the region has not been so fortunate, and most Southern states rank near the bottom of every category you mention owing to several historical factors.
The South and North were fairly similar in terms of wealth and quality of life at the beginning of the nineteenth century, but in terms of culture and education they were already fairly divergent. The driving impetus behind most of the immigration to Massachusetts and the other northern states during the colonial period was for the free exercise of one's religion, while the desire to obtain wealth motivated most of the initial immigration to Virginia and the rest of the South. Members of the numerous denominations dissenting from the Church of England scattered throughout the North sought to spread their faith by establishing schools for spiritual education. Of the nine colonial colleges the Anglican-led College of William & Mary was the only one established in the South, and it was regarded as an expensive liberality by many in Virginia.^1 A variety of obstacles including mismanaged funds and administrative conflicts prevented William & Mary from achieving the same high reputation as those schools in the North, which likely did not endear the planters of the South towards the establishment of more schools.^2 Horace Mann, the Northern reformer who founded the first free public school in Massachusetts in 1839, stressed a divine right to an education which helped spur the establishment of public schools in the North's major cities.^3 By comparison education in the South remained a luxury and status symbol reserved for children whose families didn't need them year round to work in the fields, and Common Schools would not become prevalent across the South until the late nineteenth century.^4 The Civil War also caused significant damage to several antebellum schools and colleges in the South as faculty and students went to war and battles damaged or destroyed campuses.
Although both were predominately agrarian societies at the beginning of the nineteenth century, the North grew more urbanized and populous than the South over the following decades for a number of reasons. The culture and institutions of the Southern elite residing within the coastal plain region valued leisure and relied on slaves and land as the primary forms of capital, severely limiting prospects of social advancement for recent immigrants. By contrast the North received a surge in local industry thanks to the Market Revolution, the War of 1812 and the opening of the Erie Canal in 1817, increasing demand for cheap labor and leading to an increase in urban population and the rise of the business class. While Jacksonian Democracy improved the lot of white men living in the South the immense profitability of cotton and the passage of tariffs on imported machine-based capital ensured that the success of the South's economy would be tied to the plantation system rather than major cities for the foreseeable future. The immense profits derived from plantation slavery benefited an elite few due to the increased concentration of slaves into fewer owners, who would then rent them out to yeomen for a fee (can't find my source at the moment).
The Civil War devastated the South's infrastructure, but the southern states have now had 150 years to repair themselves and most still lag behind the rest of the country for a number of reasons. The defeat of Reconstruction, the abuse of the sharecropping system, and the ensuing decline in race relations spurred the Great Migration in which much of the black workforce moved northwards, providing the North with another source of cheap labor and delaying opportunities for industrialization across the South. Wealthy rural whites maintained control of state governments through various means such as Alabama's refusal to redistrict from 1901-1960 and the use of literacy tests, all of which contributed to malapportionment and empowering a rural minority at the expense of a growing urban population. I don't want to continue past the 1950s because that's outside my area of knowledge, but hopefully that helps answer your question.
I'm pretty tired and I'm sure this is filled with rambling and typos. I'll fix them, shorten it, and add more sources in the morning. edited for redundancy.
I feel like this might be a good fit for /r/asksocialscience
It is possible that hookworm was behind part of the issue. It was a very common parasite that took away from productivity in many areas of the South, particularly among the most agriculturally fertile.