Can you help complete itinerary?

We will be visiting Japan 7 – 10 days
We would like to do the following:
Tokyo 1 day (visited previously)
Yokohama 1 day
Hakone + Mount Fuji 1 – 2 days
Nagoya + Matsumoto Castle 1 day
Alpine Route 1 day
Kurobe Gorge (optional)
Himeji + Kobe 1 day
Kyoto 1 day (visited previously)

Option 1
Day 1
Arrive NRT
Keisei Line – Shinjuku
Reason: save 2 days before the need to activate JR Pass 7 Days.
Day 2 – 3
Shinjuku – Hakone
Can you help to complete?
Option 2
Day 1
Arrive NGO
Day 2
Nagoya + Matsumoto Castle
Day 3
Activate JR Pass
Alpine Route
Can you help to complete?
We can fly in/out NRT, KIX or NGO
Can you give me suggestions how to include the additional sights in an efficient order
so we don�ft have to move our luggage every night?

Nagoya and Matsumoto Castle are 2.5 hours apart by train.

Shouldn't be done in the one day. And should have your JRP active considering the cost.

What month are you visiting?

Taking the Ltd Express Shinano from Nagoya to Matsumoto is typically 2 hours or so, not 2½, but given the approx. 5500 yen it takes, it would make sense to use the JR Pass for it if you have one. That said, the bigger question is if you even need it - if you fly open jaw you don't need the pass and adding more travel round trip just to make a pass pay off doesn't make sense. Plus if you are going to do the Alpine Route, it would make sense to add Kanazawa, which you didn't even mention. Skipping the Kenrokuen Garden would be a tragedy.
https://goo.gl/MkGZYp
You also wrote you want to see Yokohama for a day but didn't work that into your options either. And for Kansai, you didn't mention Nara or if you saw it before - if not, it is well worth at least half a day.
https://goo.gl/LfvWnL

It seems that your dilemma is that you are trying to make a plan with a completely open board - most people get their air tickets and then plan - it is a narrower, more confined set of choices that makes it easier. It is very rare that airfares to all the cities you mention and open jaw come out the same as round trip (most airlines don't fly from abroad to all those cities non-stop). Or perhaps the cost difference doesn't matter to you. Given that you want to see Tokyo+Yokohama as well as Kansai, but nothing really by Nagoya, I don't see the point of flying to NGO. Trying to avoid backtracking as much as possible is more efficient. So the best route to me looks like flying into Tokyo, seeing Yokohama and then the Fuji area, moving to Nagano and the Alpine Route, then going from Hokuriku to Kansai and leaving open jaw from Kansai (assuming the airfare is not excessive).
As for NRT to Tokyo, the Keisei is the fastest if you are going to the east side, but you mentioned you are going to Shinjuku. The N'Ex would be better if you don't mind the cost, or for cheaper, use the Narita Access bus to Tokyo Stn and then the Yamanote Line to Shinjuku.
http://accessnarita.jp/en/home/