The former colonies, as I understand, were very much against a strong, centralized American government. The Holy Roman Empire was still around at the time of the revolution, and it seems to me that that sort of government would have appealed to the founders. Was it ever suggested that the new American nation have a government similar to the HRE?
If you're talking about having an Emperor elected by the states, Alexander Hamilton wanted something relatively close to that and argued for it before the Constitutional Convention. The office of Governor would have been a lifetime position save for resignation or impeachment, and he proposed that the Governor's electors would either be themselves elected by the people, or elected by the state legislatures. So yes, it was talked about.
If you're talking about the political structure of the HRE, it's important to recognize that the decentralization and autonomy of the Princes was never a "model" so much as a series of things that happened. The treaties that comprised the Peace of Westphalia (which set down the princes as sovereign states) were just that - peace treaties to end the wars happening throughout Europe. The lack of Imperial power at the time of the Founders stemmed mostly from the repeated conflicts between Austria and Prussia, the two largest states in the Empire, which were both absolute monarchies.
With that in mind - and that at over eight hundred years old, the HRE was the oldest surviving national institution in Europe save the Republic of Venice - it's not surprising that the Founding Fathers looked elsewhere for their model.
Sorry if this breaks the rules of the sub, but why would you think that a group founding a government in direct rebellion to a monarchy would be interested in forming an imperial system? That is a Monarchy with more power given to the Monarch....