we elected to do the eagles nest first, probably could have gotten there a bit earlier, we arrived where you buy the tickets and catch the buses up ( there was 4 buses going at the same time) at about 10.am, the crowds quickly filled the 4 buses. we caught the bus at about 10.15 ( then you have to wait for the next allocation of buses)
when we got to where they let you out of the bus they ask you to select a return bus time ( good idea, i think we allowed 2 hours, we got the 12.15 bus back down) that gave us time to walk to the elevator catch it up to the building then we walked up to the top of the hill to overlook the whole area, sat around for a while, walked back to the building looked inside etc then caught the lift back down ready for the return bus trip back down to our car. (most of the other people on our bus seemed to allow the same time)
as you are near the document centre /bunkers its probably the most logical time to also visit them, however we had already done that the day before ( depending upon how interested you are this could take about 2 hours)
so we then drove down the hill back to Berchtesgaden and the short drive to the lake. parked the car, walked to the ticket office, near the lake and got straight on the boat. We elected to not get off at the church ( at the 'half' way point) but go on to Salet. we enjoyed the walk to the next lake ( with the waterfall, at the end of the lake with mountains surrounding) we then walked back to the wharf and caught the next boat back. the return journey on the lake was a little slow eg: it takes a while and people we falling asleep in the afternoon sun.
we then went and did the Rossfeld Rd.
we knew it would be a big day and was prepared to keep each part a little short. given that our day was stunning weather wise and it then rained the next 3 days, it was well calculated. something we have learnt over the years, while travelling in mountainous areas.
we did not do any cable cars etc, while in Berchtesgaden area, maybe next time.
I hope this helps.