Is there any time savings taking the train vs bus to Zagreb.
Usually I would say yes, but it also depends on the schedule (obviously if the train arrives 20 minutes before the bus leaves for Plitvice, that would be cutting it too close). When I took the train years ago, at the border agents got on the train and checked our passports as it kept moving. Buses have to stop at the border, and sometimes there might be a wait at border control (maybe not very long, but who knows?)
But I read of a recent experience of someone taking the train from Zagreb to Ljubljana where at the border they had to get off the train, get shuttled by bus to another train, and continue. No idea if this was a one-off thing or some ongoing construction or something. All kinds of things could happen. On the bus from Ljubljana to Trieste last year, even though there's no border control between Slovenia and Italy (cars drive right through), our bus was stopped at the border, and our passports taken off the bus and checked while we waited 20 minutes. So unpredictable things can happen on any mode of transportation.
Both trains and buses can be late. Some bus companies like FlixBus have handy apps that will let them notify you of delays. Last year our FlixBus to Trieste was 45+ minutes late arriving at Ljubljana, and there was really no way at the station for them to notify is (is this bus really coming???), but they did let us know twice by app that the bus was delayed but still on its way!
I don’t think that I can enjoy the scenery and trying navigate at the same time since I’m solo on this trip.
FYI, for much of the way in Croatia, you are on the A1 expressway which is inland so not a whole lot of scenery to enjoy. The best scenery is along the coast, but even then the A1 is inland til about an hour north of Dubrovnik (when it ends) and you do get some great coastal scenery. The drive to Mostar isn't scenic either. Between Mostar and Sarajevo is along the river and very beautiful, however. I drove this and was able to stop a few times for pictures. Otherwise, I would love to have taken the well-regarded train ride between Mostar and Sarajevo. But clearly you won't have the time.
Similar to other trips, I plan to take tours for my day trips (Bled) which I know are more expensive but efficient with limited time.
A tour to Bled that includes a Vingtar Gorge hike might be worth doing. If not, otherwise there are frequent buses between Ljubljana and Bled, and the lake is pretty much self-guided, so I'm not sure what a tour really adds to the experience.
I booked my hotel for Platvice, in the Park. Do any other cities require pre-booking this far out or can I book a few weeks out? Early September
I would book ahead using Booking.com to get reservations that can still be changed/canceled up to a few days before arrival (read the policies carefully, they vary by property) - nothing to lose booking ahead that way, as long as you don't forget about your reservations and either keep or cancel them later, and you can change your plans if need be. I would think early September is still a fairly busy time in Croatia even if not high season anymore, so personally I would book some places ahead.