My understanding is that because of the lack of trade regulation on a federal level (and thus states were in control), farmers were unable to sell crops across state lines. This led to Shay's Rebellion and a call for a change against the Articles of Confederation.
Now looking at the two sides of the argument for the Constitution, I see that small farmers are the ones against it. They've become Antifederalists. Specifically in Massachusetts where Shay's Rebellion started, Antifederalists hoped to win that state because of the rural farmers.
So how is it that these farmers, who were against the Articles of Confederation, ended up becoming Antifederalists who were against the Constitution? I thought they would want a federal government to regulate trade?
Your characterization of the causes of Shays' is not one I am familiar with, and I would question the importance (as well as the accuracy) of those underlying assumptions in understanding the larger picture and how rural farmers felt about the Constitution.
To reframe the facts and put it incredibly simply, British manufacturers rapidly call in debts to American / Bostonian merchants. As a result, Bostonian merchants call in debts of rural farmers. Farmers ask for debt assistance from the (largely merchant controlled) state gov't and assembly. Uprising results from state's perceived unwillingness to provide debt relief and the rural farmers feeling like the gov't doesn't represent them.
My understanding of the economics here is that the rural farmers that become rebels are largely subsistence farming. They are taking a very small percentage of their annual yields and selling them in order to buy manufactured goods from the merchants. Now, it's possible that when the farmers were asked to pay their debts so quickly these was some trade problem between states that I'm not aware of that made this a challenge. However, I do not think it is accurate to point to that as a principle cause of the uprising nor assess trade regulation as a root cause.
Again to keep it simple, this is very much a big gov't vs. small gov't dispute driven by concerns of representation. The rural farmers think the Massachusetts legislative body is largely made up of the elites that don't loo out for them (and frankly, they weren't all that off base in this assessment.) When the Constitution comes along, they fear it will result in a bigger, less representative gov't and not one that looks out for their best interests.
On the other hand, the concern of big gov't folks is that the rebellion kind of took a while to stop. The creation of stronger state to deal with exactly these kinds of uprisings is part of the motivation on their end. If you're curious about the problems the Massachusetts Governor had in putting Shays' down, I dig deeper into that in this previous comment.
If you'd like to do additional reading, the best books for Shays' are David Szatmary's Shays' Rebellion: The Making of an Agrarian Insurrection and Leo Richards's Shays's Rebellion: The American Revolution's Final Battle. Szatmary establishes the macroeconomics of it all. Richards dives more into the characters and motivations.