Approaching this question on the policy front doesn't really work, as the Federalista and Jeffersonian Republicans promoted the ideas they did for specific, contextual reasons that are no longer relevant in a 21st century economy; instead, let's look at the coalitions themselves and work up from there. In the Jeffersonian camp, you have small farmers and landed gentry, debtors, and people of a generally liberal mindset (yes, I said "liberal;" support for small government is not synonymous with conservatism); in the Hamiltonian camp, you have industrialists, businessmen, the financial interests, and anyone who profits from manufacturing and trade.
Based on these presumptions, here is my slap-together, unscientific presidential swing map:
Jeffersonian Republican 260 Electoral Votes
Federalist 148 Electoral Votes
Toss Up 130 Electoral VotesI'm not completely certain that every state is in the right column, but in general I think that the South and West would support the Jeffersonians, New England and parts of the Mid Atlantic for the Federalists, while the Midwest is a swing region. That's not all that different from the regional divide of the 1790s, actually.
As for candidates, I would expect to see a Romney-type candidate running for the Federalists and a Bel Edwards or Warren as the Republican nominee.