Hi I did a similar trip just 12 months ago up to Phong Nha - it was incredible, just amazing.
I travelled up from Hoi An taking the day train from Da Nang and then taking the last mini bus (departs Dong Hoi at 17:30, from the a bus stop near the bus station on a busy main street, not the railway station). To make you aware when you leave the railway station the taxi drivers will offer car journeys to Phong Nha for ca. VND330000, which is crazy. the local mini bus which is clean modern is just VND33000. Take a taxi to the bus stop for VND20000.
Yes I think two full days is a good amount of time. The town itself is only just developing so whilst plenty of places to eat, good quality hotels limited (I stayed at Heritage by night USD21, big room, with a pool, nothing special but friendly). Oddly I could not find any shampoo or soap for sale in the town so bring some of your own.
I did the overnight stay in the cave, which was expensive and in general you need to book well in advance as they have a limit of 16 people /day. There are however other caves to explore which I wish I had done too. Just sitting by the river is amazing in itself. So yes definitely go there! You can organise everything once you arrive, even in the evening the tour shops are open. There is a great pizza place.
At the conclusion of my far too brief stay I took the mini bus back to Dong Hoi and I flew to Hanoi. The mini bus dropped me off at the end of the street to the airport and I paid a local lady to travel on the rear of her motor bike. I appreciate you are going in the reverse direction but I would look at least a flight if possible to save some time.
I also agree, Hoi An is no longer magical. I would go back to Hue instead unless you want beach time.

