Itinerary check. Inverness, Edinburgh, Glasgow & some time in the Highlands

To answer your point about train tickets first. The best website is www.nationalrail.co.uk Here you will find links to all timetables and you can buy tickets (without commission that some other sites charge). Basically when you are ready to buy you are directed through to the Train Operators site for the purchase. Ticket prices are not seasonal - so don't expect any price reductions for travelling in September. What you will find is that there are lots of different types of tickets available, and these cost different amounts. Bascially if you want the flexibility to travel on any train, at any time then you will pay the highest price - these are 'open' tickets. There are cheaper tickets available, but these tie you to travelling either outside of the busiest (commuter) times 'off peak tickets', or on specific timed trains 'advance tickets'. The dates should open up for purchase about 12 or 13 weeks out from the date of travel. There are also a number of different rail cards that you can purchase, which then offer discounts off the ticket price. For example 'two together' or 'senior' railcards.

In terms of your itinerary, either would work. I guess it depends how you want to organise your time. You are spending quite a bit of time in cities, but assuming that's what you enjoy (over scenery and hiking etc), then that's entirely your choice. If it were me, then I might take a side trip to Stirling and visit the fantastic castle there in place of your extra day in Glasgow. Oh and unless you are tied into flights to Inverness, then in your second scenario it seems a bit counter intuitive to fly to Inverness only to then get the train to Edinburgh on day 2.
As for accommodation you definitely need to get that booked as soon as possible. September is still busy here in Scotland.

You don’t mention it, so I will. I hope you go to Culloden Battlefield from Inverness. IMHO, it’s not to be missed.
And agree with Skyegirl, you need to get your accomodations booked asap!!
Also, the three island tour out of Oban was a highlight of our 12 night trip to Scotland last summer.

I would also suggest visiting Culloden while exploring the Inverness area, and I hear good things of the Clava Cairns as well.

Just out of curiosity, what airline are you flying into Inverness? In the future I'm considering flying into Edinburgh and out of Inverness.

Thanks all.

RE Train tickets. Checking the summer schedule, I could not determine if discounted fares were even available on weekends. There is a significant difference between the anytime fares and the discounted fares, but I only see a few discounted fares and all during the week. Is that because there are so few (or any) on weekends ... or because they've already been snatched (given the busier summer)?
If we check every day for Sept. to be posted, are we likely to even see any discounted fares on a weekend (that aren't first or last of the day)? AND... how fast do the discounted fares (if any) sell? Like airline tickets, do we need to grab asap, or do we have a few days to coordinate with our accommodations, etc.?

RE Itinerary: Great suggestions so far. Appreciated.
We just grabbed some flights we thought were very reasonable, so they're set. This was a last-minute destination (for us), so we're trying to coordinate tours, accommodations, trains, etc. all at the same time. Flying INTO Inverness & OUT of Glasgow was set because other options (to/from a combination of Glasgow or Edinburgh) were MUCH more expensive than the train ticket between. First came plane, and now we're trying to figure out the "in-between".

We definitely like the countryside & hiking, but do not want to drive. Tried that a few years back in the Bath / Cotswold area. NO FUN. Our older brains just have a harder time with it perhaps. If we take trains and switch locations between cities we are constantly checking in and out of inns/hotels, and having to lug baggage. -- and we travel light (one pack ea.). So daytrips resulted as a compromise. I'd love to spend more time in the countryside... just haven't figured out how to do that yet in our limited time frame, and limited hassle.

I agree it makes little sense to immediately leave Inverness. But because planes were set, it would be an option only if it makes more sense to do everything from Glasgow/Edinburgh.

Forgot... Dave: Delta/KLM combination.

It would probably be possible to write a successful PhD thesis on the complexity of UK rail pricing! I've done a couple of sample searches on Inverness to Edinburgh using various dates in August (the latest available at the moment). An 'anytime' fare is around £45. An 'advance' fare where available is around £27. I have also found 'off peak' fares at around £35. Some advance fares are available on weekends. Until your exact dates are released for sale then it won't be possible to see what fares are going to be available on those days. I would also highly recommend doing some research on railcards so you can use them to get even cheaper tickets. Here is a link to the railcard information page so you can see what is available. RAILCARDS

In terms of when to buy then I would get the tickets as soon as they become available. Prices will never go down. The market here doesn't operate in the same way as airline tickets. The cheapest tickets will always be 'advance' ones where you are restricted to a specific train and a set time. If you miss it then your ticket is invalid and you buy a new one at full price.

Hope this helps.