I've played a number of different scenarios and I was actually looking at playing through all of them (granted I was going to go backwards) so I figured I could help out and made an account.
I haven't run a playthrough yet but the most glaring issue I see revolves around Thomas Jefferson. Thomas Jefferson is given a % equivalent to Adams in Virginia. However (assuming Washington wins the election), Virginia electors aren't eligible to vote for Jefferson because both Washington and Jefferson are from Virginia and the constitution mandates that you must vote for one person outside your state. You even mention this incorrectly in your scenario by saying that Jefferson would be ineligible to be VP rather than just not being able to get votes from Virginia. The easiest solution is to give him 0% and remove him from the ballot.
This also leads in to a deeper issue with the scenario because Clinton was the generally accepted Democratic Repbulican candidate. Jefferson was intentionally not run because of this issue (but elections being the way they were back then Kentucky didn't get the memo and voted for him anyway). In my opinion, it would be nice to see Clinton get a bit of a bump.
On a separate note, I always feel like it's difficult in the early scenarios to determine good percentages with all the lack of polling data. One thing I thought of when thinking about the scenario is house elections. House elections are results we actually have that show, somewhat, party preference. So I combined 1790 and 1792 (since the scenario starts in 1791) congressional voting data to get a potential better judge of sentiments:
F=Federalist R=Democratic Repbublican I=Party Unknown
Connecticut: 84% F 16% I 0% R
Delaware: 59% F 22% I 19% R
Georgia: 91% R 9% I
Kentucky: No info other than clearly R
Maryland: 49% R 47% F 4% I
Massachusetts: 53% F 32% I 15% R
New Hampshire: 68% F 19% I 13% R
New Jersey: 78% F 22% I
New York: 57% F 43% R
North Carolina: 70% R 30% F (based on incomplete data)
Pennsylvania: 54% R 43% F
Rhode Island 70% F 30% I (based on incomplete data)
South Carolina 60% R 40% F (based on incomplete data)
Vermont: 64% R 21% F 15% I
Virginia: 74% R 26% F (based on incomplete data)
I don't know if this information is useful. It seems to undervalue Adams which might be because he was already Washington's VP so he was just kept. Also there's little things that would need adjusting like obviously Clinton would do better in New York than your typical Democratic Republican.
I was looking for potential events or issues and the only thing I could come up with is a French revolution issue with an event that is based on an August 10th attack of Louis XVI's palace (maybe do it a few days after because the news travels slow).
You might want to add Hamilton as an Endorser as well. And I'd lower Clinton's Corruption/Integrity rating because of the issues with his previous election to be governor. Lastly, you may want to look at the relationships and make it so Jefferson and Adams and Burr and Adams because they did not like each other.