[Traveling time]
I agree with hitori that reaching Nikko at 11am sounds very late.
Wonft you leave Tokyo during the 7th hour?
Which area in Tokyo do you plan to start from?
[Nikko in late autumn]
If you travel in Japan on Monday, 24 November 2014, please note that it will be a holiday. That will practically expand the weekend from Saturday, 22 November. Many visitors to Nikko City are expected during the three days, including those in cars stuck in congestion, especially if the city is still in the autumn foliage season and the weather is forecasted to be fine.
It depends on weather conditions, but if you travel in Nikko City around 20 November, red and/or yellow autumn foliage is highly likely to be seen in the area around Tobu-nikko Station (where Toshogu Shrine and Rinnoji Temple are located); maybe it can be seen also from the twin Iroha-zaka slopes, which are known for many sharp curves.
[JR and Tobu transpirations and passes]
what restrictions apply even though I have JR Rail Pass? (if any). I fancy the trip to Lake Chuzenji and Kegon falls. Which JR pass do you plan to get? A Japan Rail Pass? Have you confirmed that the JR pass can pay off?
A Japan Rail Pass is not valid on Tobu Railway lines or Tobu Bus lines. Accesses by bus to major tourist spots in Nikko City are offered mainly by Tobu Bus Nikko. If you cannot make a Japan Rail Pass without this Nikko trip, it is worth considering that you get a Tobu Nikko Pass and make another choice for your JR rides.
A JR East Pass / a JR Kanto Area Pass is not valid on Tobu Bus lines, but it can cover basic fares and Ltd. Express charges concerning JR-Tobu through Ltd. Express trains to and from Nikko City, which are available, though only a few, from/to Shinjuku and Ikebukuro Stations of JR to/from Shimo-imaichi, Tobu-nikko or Kinugawa-onsen Station of Tobu.
Considering that you will not visit Kinugawa area, if you use Tobu Railway to and from Nikko City, I suppose a (4-day) Marugoto Nikko Tobu Free Pass can be a good choice.
: This Tobu Nikko Pass is available to any visitor, for 4520 yen per adult if you use it from Asakusa or Kita-senju Station of Tobu in November.
: This Tobu pass can be used on your accesses by Tobu Bus Nikko to and from Chuzenji area via the twin Iroha-zaka slopes. (The buses run via different Iroha-zaka slopes by directions).
: This Tobu pass is not valid for accesses to or from Kinugawa area.
A 2-Day Nikko Pass of Tobu (2670 yen per adult) is not valid for your access by bus to or from Chuzenji area. It can cover Tobu Railway basic fares to and from Kinugawa area.
A (4-day) All Nikko Pass of Tobu (4520 yen per adult) can cover Tobu bus fares between the area around Tobu-nikko Station and Chuzenji area, also Tobu Railway basic fares to and from Kinugawa area.
The latter two Tobu Nikko Passes are available only to foreign visitors, and you should use Tobu Railway from Asakusa Station when you travel with one of these foreign-visitor passes.
Unlike the above-mentioned JR East Pass / JR Kanto Area Pass, these three Tobu Nikko Passes do not cover any Ltd. Express charge. When you take a Tobu Ltd. Express train with one of these three passes, you should pay the additional charge.
If you use JR to/from Nikko Station, please note that only a small number of trains are available on Nikko Line connecting Utsunomiya and Nikko Stations. You may have to wait long in Utsunomiya Station. (I hear JR-East began voice announcement in English inside Nikko Line trains. That may help you if you travel on this line.)
[Chuzenji area]
Chuzenji is a name of a temple and a name of a lake.
I visited Kegon Fall twice in recent years, both on foot from Chuzenji-onsen bus stop. At the former time I watched Kegon Fall just apart from the outside. The latter time was during the autumn foliage season, and I utilized the elevator service for visitors to have close views of Kegon Fall.
http://www.japan-guide.com/e/e3812.htmlRegarding an access to Chuzenji Temple, I needed time more than I had expected to find a route even from the nearby Chuzenji-onsen bus stop; so I recommend checking your route in advance.