Fascinating period, and very sparsely covered - a brilliant choice.
Personally I do no more than a rough outline before I start researching, as it's in the reality I tend to find the really interesting, less well-known stuff that can give me a good story. I then start as you do, with general histories of the period. I don't note much at this stage, I'm really just absorbing and learning and trying to get a feel of what I want to focus on. Once I know that, the bibilography will lead more to more serious, detailed works on the relevant specialised areas. These can still be daunting, so it's at this stage I try to get hold of a living expert to help me get started.
For my first series (17th century France) I found one by picking the most modern of the general histories I'd found really helpful, then googling for the author under his university. I then simply e-mailed him and asked for a meeting. Real academics LOVE meeting people with a genuine interest in their specialist subject - as long as you can prove you've done the groundwork and know enough to ask intelligent, detailed questions. I came away with a list of another 20 plus books I needed to read in the first instance, but enough inspiration and ideas to find the rest I needed on my own. He also got me onto the academic list-serv where I could ask for the answers I couldn't find in books.
My second series is more modern (Victorian, starting in the Crimea) so I searched the net for the most serious research societies and made direct contact with the committee. The people I found are absolutely brilliant, and not only directed me to the best specialist works, but also spend time digitising and making available obscure letters and diaries that would otherwise be almost impossible to trace.
Either method would probably work for your period, especially as you already know the language and live in the country! But I can't overstate the value of finding a living mentor to help you through the maze. The kind of research a serious historian would put into our books would be approximately ten years per novel - so we need all the shortcuts we can get.
Once I've got the mentor I start the serious, detailed reading of primary sources - letters, diaries, contemporary newspapers, official records and dispatches - as well as the most highly recommended specialist works. What I do try to make sure of is that every primary source is balanced by another - especially when I'm dealing with a political or military subject which inevitably has two sides. Only reading an English (or Scottish) account of a battle is like only reading the Daily Mail and believing that's an accurate record of British thought.
The other really important lesson I wished I'd learned a bit sooner is that at this stage you really MUST take notes of those obscure details you think you'll want to use - and crucially with page references so you can find them again quickly. You'll need them when you're double-checking as you write - and your copy editor may well ask for the source when you're prepping for publication. We all know the frustration of those 'Ah! Wait a minute, didn't I read somewhere something about....' moments when you have to look back on 120 books and try to remember which of them had the bit you need....
It's from this detailed reading I'll probably start to get a real shape of what I want to do. At this point I usually start writing - and stop after two sentences because I realize I don't know exactly what my hero's wearing, what's on his trencher, how his room is lit or what's on the floor. More reading follows of the 'general type', and often a certain amount of searching on the net. I'm pretty sceptical of amateur websites (ie ones where I don't know the credentials of the authors) but sometimes these can be goldmines. When I do find something I want to use, I'll contact the site-owner to ask for his source. If they're any good they'll answer - if they don't, have nothing to do with them.
For general background of this type I'll also approach re-enactors. There are FARBy types out there, but the hardcore guys are really wonderful - and there are several Scottish groups for your period you can find with a quick Google. Go along and play with them if you can - no reading is a substitute for making fire with flint and steel or experiencing the weight of heavy armour.
It's also about now I'll start visiting the locations - though I usually have to go again when I know exactly what I'm looking for, eg the sightline from x to y. I'll also visit museums, and the one tip I'd offer on this is to write or phone first to let them know you're coming. If you can show good knowledge and know exactly what you're looking for, the curator will often make time for you personally and even get artefacts out of back rooms to show you. Warning - some of them are too damn interesting to be safe, and I've been to one place looking for details about buttons and come back with a whole extra subplot.
It's for these last reasons that I keep writing all through. Just because we do historicals doesn't mean we're not prone to the same vagaries as other novelists, and our stories have a habit of changing at the characters' whim, or at the latest twist of research. It's a constant chicken-and-egg thing with me - I can't write till I've researched, but until I've written it I don't know exactly what research I really need. So after the prelimary months I just do both, adjusting the writing as other things change.
Some things never change, of course, and I keep the most commonly used bits of research tacked up on walls all round me - eg how many miles can a horse ride in a day. I also keep on the desktop the inevitable day-of-the-week cribs so you don't make Catholic characters eat meat or mend a fence on the wrong day, and a big red sticky to warn me when Lent, Easter and crucial Saints Days fell in the relevant years. I also do maps after visiting the locations and these go on the walls with photographs to remind me as I write.
This isn't necessarily a good template, and I'm sure there are more efficient ways than mine. I'd be really interested to see how others approach your question, as I suspect I have much to learn!