Now I have to decide if the convenience of a pass is worth the extra 35 or so EUR. I worry that we'll miss a train and then have to buy another ticket at full price.
As we already noted, since we counted that extra not tied to a specific trains (but chosen randomly), then the best thing for you will be just to recheck for your desired connection on your desired date. Than you will exactly now "the extra" and can make your mind.
Is it very much trouble to make a reservation? Can it be done just before we get on the train?
It is not very complicated thing, but you might encounter some queues and potentially even "fully booked" trains (really depends on time and date), especially since there is a limit for passholders.
TrenItalia website as well offers reservations for passholders online, when selecting a price of your journey, you need to click on "more fares" and chose "Global Pass".