Hi Ajay - Here are some partial answers, to get you started
1.- Your schedule is reasonable and can be done with 4 and 8 year old children. That will be especially true if you use the luggage transfer services as noted below. Although you can certainly take tours, you will find quickly that you do not need them.
Since you are not rushing to crowd a whole lot of things in each day, the connections will not be a problem. If you miss one, there will be another train along....in half an hour often on well traveled major routes, and in all cases on well traveled routes, after one hour. All of your routes are well traveled.
The stations have good signs. In the major stations, luggage carts are available for a returnable 2CHF deposit. The carts work on escalators and there are elevators, too.
Interlaken Ost may be the exception....it has been a few years since I went through IO, but i recall narrow stairs and no elevators for changing trains. Perhaps Arno or Annika can amplify. If true, all the more reason to have your bags shipped.
If you were going out into the countryside in farm country in some regions, there may be a mid-day gap of an hour or two bus or local train service, but you will not run into that.
I would strongly suggest that you carry small bags and send large ones ahead by rail to Luzern and Interlaken.
Although the costs can add up, at 12 CHF per item, your itinerary is ideal for that. Only 3 or 4 transfers.
The trains from the airport to Luzern have many travelers with baggage. They are almost always double-decker cars with a large entry level with the platforms are where you can put your bags, as well as luggage racks in some of the compartments. You could try that with your bags if you wish....Airport to Luzern is once every 30 minutes; one train goes direct, the other requires change of trains at Zürich Main Station. That connection might be tight with luggage , but there are other frequent trains to Luzern.
If you want to get the direct train, and have to wait, you can wait in the food court on the street level of the airport train station and have a bite to eat or a cup of tea if you wish.
See attached screen grab. It is for July, but the schedule is the same for June.
Note that track numbers and transfer times are shown if you expand the entries by clicking on the "+" sign to the left of the journey.
Since you will not carry luggage on your scenic excursions, all of your connections will be easy to make within the allotted time....or, wait for the next one if you miss.
If you wish to take the time to get a printed itinerary at a station, the ticket agent can print one out for you for your excursions. Or, you can prit out some options at home.
In the Jungfrau Region, this map may help you visualize the journeys. The connections are obvious.
I have turned on train and cableway stations using the menus under "Points of interest."
5.- Luggage at stations.
Lockers are good for 72 hours, as you have noted, and then the luggage is transferred to the Left Luggage Office, where it begins to accrue a per day storage charge. Or, you can leave luggage at the Left Luggage office at the main stations. If you ship your luggage ahead, it will be held for you at the left luggage office. If they hold it for several days, it begins to pick up daily charges.
Most hotels will hold your luggage. Some smaller ones may not have a lot of space, but I have never had a hotel say "no."
2.- I cannot advise on hotels. Arno and Annika know a lot more about that. Hotels in large cities are certainly expensive.
Under the listing for major cites in this website there are suggestions for accommodations.
Yo should definitely post a new query in the Accommodations Forum, listing your dates and locations.
If you think June is bad, wait until July and August. Those are school holiday months. Although I have some favorite hotels, they are on the expensive side. If I wish to save money, I find a village on a train line with service every 20 or 30 minutes, or a bus line with frequent service, and stay 15-20 minutes ride outside the main towns. Actually I really prefer to say well out in the countryside,45 minutes or an hour from the cities, because i like to walk on the hiking trail network, and I take day trips to the cities.
Here is one example of staying just outside a major city:
Still not the cheapest, but it illustrates what I mean.
Arno or Annika may have some ideas
Item 4 -
Cheapest ForEx commisions are at banks and at the train station service exchange windows. Don't use Travelex...much more expensive. If I recall correctly, all banks give the same rate.
Most people find that using their credit or debit card to take money from the ATM machines run by the major banks...UBS, CreditSuisee, Raiffeisen, Zürich Kantonal Bank, and the Swiss Post Office give the best rates, also.
All of this can be overwhelming from a distance, but once you are on the ground, it will go smoothly. Switzerland wants tourists to be happy, and works hard to provide good services. Unfortunately, some of them, such as the luggage transfer services, can cost bit.