I just have a few things to add that I hope will further assist you.
>> If crowding can be an issue, is it worth the extra for first class to ensure seats, etc?
In my opinion, yes. I prefer to travel first class when trains are crowded if I have my suitcase with me. I usually travel second class, and just upgrade to first class for a particular sector. You can buy a first class upgrade from the ticket window just before travelling, or in the SBB App if you have mobile internet access and have set up an account with SBB. The cost is 50% of the difference between the first and second class fares if you are travelling with a 2nd class Swiss Travel Pass.
The Swiss Timetable will give an indication of expected occupancy for many routes. Morning and evening commuter times between cities are usually the worst, and then July is peak tourist season.
In July, I would expect the Luzern-Interlaken sector to be crowded for most of the day. It was quite crowded even in September last year.
>> Is the Glacier Express worth the extra expense or are the standard trains (nearly) as good as I assume they must travel on the same line? If worth doing, is it possible to include a trip on the Glacier Express when transferring from Interlaken to Zermatt?
The regional trains travel along the same route, but don't have the panoramic windows. The standard windows are perfectly OK for viewing the scenery if you have a window seat. I have attached some photos showing the panoramic and normal windows.
If the only sector of the Glacier Express you would be doing is from Brig to Zermatt (which would be the logical sector in transit from Interlaken to Zermatt), I would not bother with the official Glacier Express for two reasons:
1. The first Glacier Express of the day in the direction of Zermatt will not arrive in Brig until 14:45, arriving in Zermatt at 16:10, which limits your options for activities in Zermatt on your day of arrival. If you take regional trains, you can get to Zermatt hours earlier.
2. In my personal opinion, the best part of the Glacier Express route in any case is beteen Andermatt and St Moritz.
However, if this is the only time you are ever likely to experience a train with panoramic windows, it might be worth it to you to pay the reservation fee to travel on the Glacier Express, and arrive late afternoon in Zermatt.
For getting from Interlaken to Brig, regardless of whether you take a regional train or the Glacier Express from Brig, I would recommend the route Interlaken Ost to Brig via Kandersteg, which is a scenic route and avoids the Lötschberg-Basistunnel. Routes via the Lötschberg-Basistunnel are faster, and will be the default route suggested by the Swiss Timetable, but you miss some very lovely scenery. To get the scenic route to display in the timetable, you need to put "Kandersteg" into the "via" field. The sector Spiez to Brig is likely to be pretty crowded.
>> Lucerne Lake cruise – we would like to do the ‘Classic Round Trip’ or similar - is there plenty of availability so that we can book when we arrive, or would it be better to do this in advance?
Instead of a round trip, I would recommend a one-way trip the length of the lake between Luzern and Flüelen. This will take almost 3 hours, and you can take a train back to your point of departure (about 1 hour).
As the boat is likely to be crowded in July, and reservations are not possible, you could consider getting the train to Flüelen, then the boat from Flüelen back to Luzern. This might be less crowded than starting from Luzern, as long as you avoid the boat departing from Flüelen at 14:00 (which is part of the Gotthard Panorama Express trip and will almost certainly be crowded).
>> Pilatus ... location of bus stop in Kriens
The bus stop near the Pilatus gondola is called "Zentrum Pilatus". Please see attached screenshot from Google Maps showing how to get to the Pilatus gondola. In the direction from the bus stop to the gondola, the walk is slightly uphill.
>> Interlaken - Jungfrau – We would like to do the ‘Jungfrau One Day trip’ or similar – would this need to be booked in advance? Would it be possible to include a trip up the Jungfraujoch as part of this trip or would this need to be done on a separate trip due to the time needed?
Personally, I would make a trip to the Jungfraujoch a priority when you are in Interlaken, and then fit in other things around it as time permits. As this trip just involves getting trains up and back, it can easily be done on your own. You can go up via Grindelwald and back via Wengen (or vice versa), and I would recommend you do this to experience the very different scenery on each route.
Reservations cannot be made between Interlaken and Kleine Scheidegg, but I would recommend getting a reservation for the trip between Kleine Scheidegg and the Jungfraujoch, as it will be very crowded in July. Don't make the reservation until the day before though, so you can be sure the weather will be suitable for going up. If the Jungfraujoch is in the clouds, there is no point in going up there, but a round trip to Kleine Scheidegg via Wengen one way and Grindelwald the other way would be a great experience if they are not also in the clouds.
>> Trip to Thun – is it best to visit Thun by train, or is a boat cruise the better option? Is this easy to book when in Interlaken, or should it be booked in advance?
What are you intending to do in Thun?
>> Zermatt Matterhorn trip – we will probably take the cogwheel train via Gornergat (though is it worth returning via Kliene Matterhorn for different views, etc?) – how long would we need to allow for this trip?
The attached map showing the mountain transport in Zermatt illustrates why you can't go up via the Gornergrat and back via Klein Matterhorn.
I hope this helps.