So if you have Washington dead, and Jefferson come back, then maybe you could work this out. I don't think that Adams was all that appealing of a candidate, and Jefferson was the author of the Declaration of Independence, so I think that if he was back from France then he could be President. I would say that you would have serious problems nearly immediately with President Jefferson's administration. Jefferson was very much a states' rights guy, even given his use of extra-constitutional powers during his administration. I don't think he would support Hamilton's financial plan, and he would pursue good relations with the French. I think the result would probably be a very, very brutally partisan environment (even more-so than OTL), though Jefferson may be able to survive the 1792 election.
Without Washington to push Hamilton's policies, then I think that your going to have a hamstrung government. Federalists (or proto-Federalists) will dominate the Congress, but Jefferson will mostly oppose them. Hamilton will probably be in Congress, rather than in the Cabinet, and end up leading the opposition. Adams will not like what is happening and could bow out in '92 and instead be appointed to the Senate.
I think that you will end up with much more fractured American politics, and the possibility that another Constitutional Convention needs to occur. Or Alexander Hamilton pulling a Napoleon. Actually, I think this is rather likely with a Jefferson Administration 1788-96 (and possibly longer).
The Whiskey Rebellion happens anyway, Hamilton raises an Army (an extra-legal Army mind you) to crush it (claiming some kind of legal justification through a most creative reading of the Constitution) and crushes the rebellion. Then Hamilton wheels the Army around and marches on Philadelphia in order to end the rule of the "Jacobins". There is huge public support for Hamilton's move, particularly from the moneyed elite who resent Jefferson's economic policies and fear his pro-French attitudes (the Terror is happening in France as the Whiskey Rebellion is crushed).
Hamilton declares himself "Acting President" or something and seeks to unilaterally add a few new amendments to the Constitution. The result is that Hamilton basically ends up a sort of Cromwell figure, ruling like a King in an imaginary republic. His economic policies curry favor with the moneyed elite who OTL supported the Federalists, and his anti-French policies, which include war against the French (which ends up really being war against their Spanish allies- to gain Louisiana and Florida), curry popular favor.
Hamilton is able to maintain his rule for a number of years, eventually calling for a new Constitutional Convention that passes a Constitution that is much more "stable" than the old one. This constitution features Hamiltonian favorites like life-terms for Senators and the President, and an emasculated House. Since Hamilton is already President, its rather conveinent. The state governments generally accept the new Constitution and the Senators are appointed. Though some rail against the system, in general it is accepted by those who hold power within society.
The capital will definitely stay in Philadelphia.