Fit in Verona, Bologna?

My honest opinion? It works the way that you figured it out for yourself:

Milan (2 nights), Verona (2), Venice (3), Bologna (2) & the CT (3) + Florence (3), Tuscany Agiturismo (4), Assissi (2- Easter) and Orvieto (1)

If it makes sense to you and you know what you'd like to see and do - go for it! :-)

We spent 2 nights in Verona and we saw quite a but. I haven't been to Bologna so I don't know if that is adequate time there. I think the new plan looks good.

You have told us you land in Milan, but where do you depart from to return home. From Milan?
If you return home from Milan you should leave your nights in Milan to the end of your trip therefore:
Milan (0 nights) go straight to Verona
Verona (2 n.)
Venezia (3 n.)
Bologna (Bologna is a half day visit, do you really need to spend any nights at all? Skip and stop for half day while on route or no more than 1 night).
CT (3 nights)
Florence (3 nights)
Rent a car in Florence.
Tuscany Agriturismo (4 n.)
Assisi (2 n)
Orvieto (1n, but you could add another if you intend to visit Civita also).
Return car in Orvieto.
Train from Orvieto back to Milan (if you fly out of Milan).
Milan (2 nights max, 1 full day is plenty for Milan)
Depart to go home.

Thanks everyone for the feedback. Guess I did leave something important out.

We plan to start our Spanish leg on April 23rd with a flight from Rome to Barcelona. Based on advice from Roberto and others, we'll drop car in Orvieto the day before, spend the night, and take the train in to FCO.

I would like to visit Civita. Roberto, you think a 2nd night in Orvieto is important for that?

Thanks again

One night in Orvieto might be enough for both Orvieto and Civita. But if the next day you fly out, you may not have time for both.
Since you are flying out of Rome, I guess Milan must be visited upon arrival. However do you need two nights? If you arrive by noon you can visit Milan in the afternoon and the next morn before heading to Verona.
The train trip from Orvieto to the Rome airport is about 2+ hours (with change at Roma Termini). You can spend the night before in Orvieto if the flight is later in the morn or the afternoon. If early morn, you might have to sleep in Rome.

I like your revised itinerary. A night or two in Bologna will give you more time for great food!

Or, you could see Bologna as a daytrip from Milano. I guess you could do the same for Verona from Venezia. Check trenitalia.com to see if that is more convenient than adding two more hotel changes.