Golden week means the 1 full week, Japanese are having holiday.

Same story as if we have long holiday in Malaysia. Most places will be crowded. Even accomodation also hard to find.

No place to sit/stand in train

Japanese are Holiday too.
Transportation will be fully booked. Almost impossible for you if plan to City Hopping.
Onsen Village area such as Hakone will be very crowded.
Hotel price will twice expensive.

I m renting this unit from Midvalley/KLIA ... for my jp trip in March... Unlimited Data usage in JP.
http://visondata.com.my/plans/japan

Never used visondata. Currently, I have booked travelrecommends wifi since they are doing promotion at rm15/day on my trip to Japan next month. Will do a review posting once I have tested it. But judging from the screenshot and devices, it should be either au networks or y mobile

Yes, RM15/day nett.
No hidden charges, Unlimited data quota, but you will required to pay RM200 deposit  which will be refunded later and you can collect from KLIA terminal or they will send the device to your home few days before your departure.

Tokyo Subway Ticket (1-day: 800 yen, 2-day: 1200 yen, 3-day: 1500 yen)
Unlimited use of all subway lines (Toei and Tokyo Metro). Not valid on JR trains.

JR=Japan Railway, company name. Different lines has different company running it.

your trip: all in one day? or two days or 3 days?

one night??? Just forget about pass. Individual tickets give you more flexibility. You are taking 3 trains, which average is about 180yen.

Too rush. Tokyo most shop closed at 8pm, mall closed at 10pm. You start your trip at 6pm, one akibahara enough keep you stay until 10pm. Your plan are suitable for one whole day.
Unless you reach station take some picture then hop into another station.