Sorry, I did not reply directly to your dilemma.
It is theoretically possible to catch the 0810 cable car ( die Luftseilbahn) from Wengen to Männlichen, walk quickly to Kleine Scheidegg, get a train to Jungfraujoch ( not crowded. short or no lines in September) , go up, go back down to Grindelwald and up to First ( 2 hour trip) walk to Bachsee and return ( 2 1/2 hours) and catch the last cable car down from First at 1730. Too rushed, dependent on perfect connections, no time to stop, and you absolutely don't want to miss that last cable car at First.
I would not try to do it, and I know the systems. And, since I take a lot of photographs, I could not even accomplish it.
So, I'd take the option you described. Männlichen , KS, Jungfrau on one day in that order. Pick a day with pristine weather, or maybe skip looking at the inside of expensive clouds at Jungfraujoch.
On the way down, you can consider a few options, depending on your wish to walk or ride.
www.swissholidayco.com /Public/Assets/User/fi les/Map-of-Jungfrauregion1.jpg
And, you might pick up time to see Trümmelbach and walk a bit on the LB Valley floor, if it does not all come together on your first day at Schilthorn.
Do the Bachsee walk on the other day, via the cableways as you described.
I offer this perspective:
1.- If the weather is not clear, don't go up.
2.-Relax your boundary conditions, as the engineers say. There is no harm in a little backtracking. The sights are good enough to see a few of them more than once. Look to the left on one pass; look to the right on the second pass. ;-) Part of being there is to kind of soak up the general ambience, as well as to check off specific places on a list.
And, face it, you can't see it all in days...think weeks, especially if you allow for weather.
3.- September can offer really great clear days.. Some of the attached photos were taken in September 0209, when my daughter and granddaughter came to Switzerland with me. Although clouds do tend to gather at the Jungfrau in the afternoon, you have a good chance of no problems in September. The allusion to the Grannie's Walk is to the nickname for that walk from Männlichen to KS.
4.- Make your trip to the Jungfrau region as early in September as possible. The whole month is usually good for weather on average, but the chances are best earlier in the month. Those attached pictures with daughter and granddaughter taken on approximately September 25th, but we watched the weather for a week and picked our day.
The one of the LBV from Wengen was taken late enough in the year to have some color in the foliage, and the waterfalls had thinned out; no Spring snow melt to feed them.