Finally, how much hassle is involved in the M1 student visa application process? I have a C1/D which required a letter of employment, will I need a course confirmation letter from a US school first, or do I apply for the visa and then find a school?
To get an M-1 visa, you first need to find a school, and that school needs to be SEVIS approved. There are two types of flight school in the US, part 91 and part 141 (I think those were the numbers - not sure). One of those is automatically SEVIS approved (I think that's the part 141 schools - again not sure, I always mix these up) but the other type usually not. In any case, all the schools that do JAA training in the US are SEVIS approved.
You enroll with that school, and they will "sponsor" your visa. Which essentially means that you get an official piece of paper from them saying you're enrolled. With that piece of paper and some further paperwork (plus a photo conforming to US standards, which are different from EU passport photos) you make an appointment with the US embassy or consulate, who will then issue you an M-1 visa. Note that getting the appointment may take a long time, and the appointment itself is a three-hour affair too (in my case - wish I had brought a book).
However, in your particular case, since you're the holder of a C1/D visa, there might be a chance you don't require an M-1 visa. After all, an M-1 visa is required if your primary purpose for the visit is (flight) training/education. But if you go to the US regularly for the main purpose of whatever you got the C1/D visa for, and you do a few hours of flight training on the side, flight training is not your main purpose and your C1/D visa may suffice, subject to any specific limitations in the C1/D visa.
BUT this is not the default situation for a lot of flight students and you might need a little supporting paperwork (or the verbatim legislation) from the USCIS saying that this is indeed allright. Don't trust the opinion of just some anonymous blokes on an internet forum on this. Because if you (we) do get it wrong, you might not just end up in conflict with USCIS but also with the TSA.
Speaking of which, if you do flight training in the US for an "initial airmans certificate" you also need TSA clearance since you're not a US citizen. This is regardless of the exact visa you're going to need.