I do not think you will have any luck flying into Visalia. You are probably better flying into Fresno and taking RT 180.
All the place you are thinking about seeing are worth while. I enjoyed both the caves a few years ago and they were great. You will not be able to see Mt Whitney unless you are on the other side, the east side of the Sierras. You would have to get to it off Rt 395. You would have to take 99 south to 58 east to 395 north, maybe a 300 mile drive.
The color in October depends on the year. However you probably will not see much unless you are late October. The water in the rivers will also be low or gone so the falls will not be very good, unless we have a better than average snow pack. The good news is that the tourist tend to slow down after labor day.
I have not stayed at the Muir Lodge but have heard good things about it.
Feel free to ask any other questions. Hope my answers helped some.