I'd echo some of stut's comments.
Sounds like you want a bit of a mix, and fair enough. Although Scotland's outdoors is beautiful, it's cities are great. I love Glasgow and Edinburgh, although in different ways. I prefer Glasgow - more of a real city and less touristy. The nightlife is also better. But then Edinburgh's just lovely and you can't miss it from your itinerary.
Unless you have a personal preference to head for the highlands/further north in Scotland (in which case a flight to Inverness would be a good idea), I'd get the train to Glasgow to start with. One day/night is enough to get a flavour of the city, from where you can hire a car and drive north. I did just this with a group of friends for a holiday several years ago - our destination was the Ardnamurchan peninsula. Lovely scenery and the drive from Glasgow was pretty good. Very doable in 3-4 hours so great for a day and a stop on the way (you pass by Loch Lomond on the way too).
Ardnamurchan is also the most westerly point of mainland Britain. Little-known fact! Also, it sets you up for a side trip to the Isle of Mull. A drive back and one or two nights in Edinburgh and you have the basis for a great trip.
Two other bits of advice I'd give: one is be prepared for midges in rural areas at that time of year (midges are small mosquitos). In general it won't impact your day with a bit of protection. Except from about 5pm for an hour when you definitely want to be indoors.
The other is to spend some time choosing your accommodation - and book well in advance. You have plenty of options from B&Bs to camping, glamping, woodland cabin type things and loads of others. I'd personally find a lochside cottage/cabin with decent facilities (fully equipped kitchen, wifi etc) and base yourself there for several days and explore day-by-day. But that might be more a personal thing. Bear in mind for self catering especially, that in these more remote areas you can be a very long way from the nearest shop, so best prepare.
Enjoy! I'm sure you'll have a great time. Come back and tell us what you've found
