I understand as guest in Tokyo it would be rude to ride the subway and the rails from 6am to 9am on weekdays? same rules for weekend? What are the no go hours for afternoons.

Train distance time rules? If I ride from Tokyo station to Omiya,no exit and back Omiya to Kanda that would be about two hours? Would that attract unwanted attention at the exit ticket gate? Is it best use an ic or paper ticket, any difference

Thanks

Not so much rude as taxing for you. Weekday commuter trains are nicer to ride after 9am and usually get crowded again from 5-6pm.

Assuming Tokyo - Omiya (Saitama) - Kanda (Tokyo) on regular JR trains, the trip will take about an hour's ride at most.

If you will be riding daily and/or moving between the various train and Metro networks, an IC card (Suica or Pasmo) would be best for the convenience and flexibility.

You should have no issue getting through gates if you exit one stop from Omiya. You can then take the next short train ride to Omiya.

As said above, again, not rude, but might be difficult if you have luggage with you, as it can get quite packed. On the weekends there isn't too much in terms of rush hour, but the last trains of the night tend to get pretty tight depending on where you are.

For two hours within the system you'll have no issues. It'd only be a problem if you exceed 24 hours on a regular ticket or somehow leave the system without tapping an IC card or inserting your ticket into a ticket gate. IC cards tend to get a slight discount on fares (1-10 yen depending on the distance), and honestly they're a bit more convenient than having to queue up each time for a paper ticket and trying to read the fare chart, so I recommend using one.

I don't get it.

Public transportation is for any paying customer at any time when it's running. It's not rude for you to use it. In any case, peak commuting hours do not start at 6:00 AM. From shortly before 8:00 AM to shortly after 9:00 is probably the most crowded time - depending on where you are.

There are no "no go hours."
Afternoon peaks are spread out over more hours. You might find crowded trains back to the 'burbs from 5:30 PM to 7:30 PM. There are later evening peaks on paydays and during seasons when companies have celebrations etc. Now that I think about it, the cars on those trains can become "no go zones" at times.

I think probably a bit less than two hours. You can find journey times on Google or Hyperdia.com
As long as you ride trains that don't require a supplement, your ticket is usually only checked at the gates.
IC is generally better than paper tickets since you don't have to calculate fares.

The Hawaiian sumo wrestler Takamiyama used to ride the Yamanote Line which circles Tokyo for hours in a depressive state:
Kuhaulua reaches career's end | The Honolulu Advertiser | Hawaii's Newspaper

Trains do not run through the night.

During peak hours, depending on the line/direction, you really have to squeeze on the subway

its normal, regular commuters do that. Just note that it'll be nearly impossible to bring your luggage with you (trying to do this would be rude)
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