1. I'm also planning a similar trip, but I started with 12 days as my base plan. Enough or not is up to you. I've seen 7-day itineraries from Osaka to Tokyo. Depends on whether you're the type who prefer to visit a lot of places in one day or you like to spend as much time as you can in one location. If you just hit the main attractions, I think it can be sufficient.

I usually prefer portable WiFi because can share. And I always carry a backpack anyway. Plus I keep my own mobile number active, for just in case.
What I'm interested in, is how cold is November in Tokyo? Need prepare long johns? For reference, I find Cameron Highlands to be not cold at all, maybe a bit cooling during rain or at night.

1. 10 days will be a bit rush. I stayed 9 days in tokyo few months ago and it is barely enough, and I only visited one shrine/temple only which is the sensoji temple. Others, not interested. But since you've already booked, so you just have to prioritize which one you really want to visit.

2. Cant comment for JR pass but for Tokyo, a suice/pasmo card will be able to cover most of your travel around central tokyo.

3. I stayed in hotel and honestly, very hard to find a decent and convenient hotel at Rm200 per night. Mine is around RM400+ per night but location and only 3-5 mins walk to metro station.

4. I went to Hakone to view Mt Fuji. actually it all depends on the weather. If there's clear skies, you can view it from observation decks in some of the buildings in Tokyo. If weather is foggy, you can't even view it in Hakone. I only saw it clearly on my way to Hakone in the morning.. after 10am, it is already covered by fog.

5. Mobile wifi is better and cheaper, especially if travelling in groups, can split the cost. If you use simcard, other people won't be able to use it, or if u hotspot, your phone battery will go flat very fast.

We're prolly somewhat of a same kind then. I am not a temple guy myself since I go around for food and views. But i do go to some parks since they have breathtaking views.
A bit of advice, bring a sweater along if you're staying out later than 7PM. It may not be so cold during the day, but when it gets dark the chill gets so much more intense. A down jacket would be nice since it's space friendly.

As a foodie, I winced at your duration for Osaka and Kyoto since they have awesome food, view and attractions.
Then again.. I do not know the focus of your trip so.. yeah..
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About Nara.. as I did not visit temples as much(still visited a number of them in Kansai) I don't find a lot of interesting stuff there. If you don't care about temples and deer, might as well skip it.

I got my pocket wifi from Wiyo when they promoted RM14 perday for Japan. It's now RM20 tho.. They'll call, meet and give you the device before your departure(you state the date and time) and they'll call you to pick up when you arrive.
If you departure/touchdown at KLIA2, it's self service at their counter for both pick up and return.
Some other providers are offering RM15 per day but I can't tell about the service. Just read through their rental steps and you'll be fine.

If you plan to go to Onsen, one option is Atami which is between Kyoto and Tokyo, though its much nearer to Tokyo.
Its cheaper than Kawaguchiko and easier for you to access from Kyoto and depending on luck, you might get a view of Mt Fuji too. Dont think a lot of tourist goes there but for Japanense its famous for its onsen.

Typically late March to early April.  Some place may carry on to mid-April.  It depends on the weather that year.  This year sakura bloomed a bit later.

You can see the chart of sakura locations for 2017 ...

Hanami Japan: Popular spots 2017

have anyone here booked hotel rooms via airasiago?

is it based on the room price or price per person?

coz airasiago display price per room, scared that if i purchase the room rightaway, sampai sana suddenly got extra fee to pay

"Overrated" or not depends on individual likes or dislikes also leh. Example I'm a huge aquarium fan so I really enjoyed Osaka aquarium even though it's not really better than Aquaria KLCC or Singapore's aquariums.

Then in Kyoto I visited the geisha dance thing (miyako odori) and it was interesting for like 5mins and then boring as heck after that -- but cos i got no interest in that kind of thing.

Bro I stayed in granvia osaka hotel got discount tickets to kaiyukan and USJ. Anyway is already paid with those room prices.
Even the train nozomi Osaka to Tokyo also discount. Some of your advice is so true. You cannot feels the speed how fast. Just save time in 2hrs+ arrived Tokyo and can see mount fuji along the way.

1. the notable mention is the top floor observation floor, where u can see the surrounding. other than that, its museum n historical stuff. nothing much mentioning.

4. i would spend more time at Kyoto, for the nature n historical building/temple.