Pauline Maier "Ratification: The People Debate the Constitution" is an excellent source for both of these questions.
With respect to your first question about economic differences, consult any discussion of the Bank of the United States, the arguments between Hamilton (who argued for a commercial country) and Jefferson (who argued for a pastoral anti-commercial country). Southern states were nearly hysterical in their fear of "Northern Stock Jobbers". Or consult the controversy over the Jay treaty that almost sunk the country before it started (briefly, Northern states were willing to trade away the Mississippi in exchange for commerce, while Southern states were horrified that we would make any compromise with Great Britain.
State vs Federal rights. This was one of the chief impediments to the passage of the constitution. One of the centers of opposition in all states was by people who feared what would happen if the constitution were passed without a bill of rights limiting the power of the Federal Government. Pauline Maier's book, and Jack Rackove's lectures on iTunes are another excellent source.
Your question ignores several obvious sources of evidence. Look at the compromises needed to found the country - each of these were issues where the two sides were willing to fail rather than give in to the other.
- Bicameral legislature - The legislature could not be formed on the basis of population nor on states. This is a key source for "states rights", but it is based in part on population counts vs development & commerce. Virginia argued for a legislature based on population, while the North pursued the Connecticut plan based on state representation. Randolph and Madison propoosed the compromise, but both sides were eager to walk from the table rather than to allow the country to be formed on the principles of the opposition.
- The 3/5 compromise - another "walk from the table" where both sides were very aware that compromise could imperil their way of life. There is a reason for Section 9 of the constitution which forbids consideration of slavery until 1808; they knew that this was an issue that would fracture the Republic if considered too early.
- Location of the Capitol. The first two capitols were in the North (Philadelphia, and New York) The South wanted the Capitol in the South. Jefferson and Hamilton reached an agreement that the Capitol would be established in a Federal District near the boundary between North & South. (technically teh boundary was the Mason Dixon Line, but Virginia has always considered itself not just the center of the country, but the center of the Universe).
There is ample evidence that the founding fathes saw the potential for future conflicts. You extended the question to ask whether they foresaw civil war. That's a bit more subtle, and I'm not sure what you mean. They had seen Shay's rebellion (over the rights of rural farmers against commercial interests), the government held hostage in Philadelphia by soldiers. They had to force Rhode Island to join the Union (not by force of arms, but I think it is relevant). Within a few years Burr led a seccessionist conspiracy, one of the other Northern states tried to secede, and Jefferson was created West Point because he feared the military might of the Northern states.
Yes, they foresaw the country splitting back up into states, and that would very likely engender conflict (in the short or long term, low intensity or high intensity conflict).