Hi, Steve...
Thanks for your contribution... you're not wrong in what you say about the standard operational code of Kü.Fl.Gr.506 being 'S4', but Junker is also correct in differentiating between Stkz and Vkz.
By way of explanation, an alpha-numeric code for say, 3./Kü.Fl.Gr.506 may have been S4+?L, where '?' is the individual aircraft I/D, and 'L' the indicator for 3.Staffel. This is a Vkz - Verbandkennzeichen, which we might take to be the code of an operational front line unit.
A code such as the one applied to this Ju W34 (See), PQ+AG, is a Stkz - Stammkennzeichen. As I understand it, these were allocated by the factory building the aircraft. A block of codes, ie PQ+AA to PQ+AZ, would not necessarily have been applied entirely to Ju W34s, although any given portion of codes within the block may well have been allocated to one type, built by one company. This complicates matters as it is rarely possibly to presume, for example, that the aircraft preceding or following the one in my photo - PQ+AF or PQ+AH would also have been assigned to the same unit since the factory would allocate codes as the aircraft left the production line, but the first one may have gone to a training unit, the fourth to a test centre such as Rechlin, and yet another within the block of codes to say, a fighter unit as a liaison aircraft. I suspect that was the role of the aircraft in the photo, where it clearly shows a Stkz, but also the unit insignia of an operational front line unit.
If you're looking for more information on the different types of code, I can recommend the LEMB's Stammkennzeichen database,
http://www.luftwaffe-experten.org/stammkennzeichen.html. LEMB is another very good website with a forum, if you're not already aquainted with it. The database is a free access one. It is not a complete list of codes, but it is a list of known alphabetic codes, and also the civil-registered nationality codes, 'D-xxxx' and the Wermacht-Luft 'WL-xxxx' codes.
In addition, you can try
www.luftarchiv.de, and from the left side menus, select the following: Luftfahrtindustre, then Motorflugzeug, then 1939.1945. There you will see the standard structure of operational front line unit codes, with their appropriate colour coding as well. I doubt German is overly necessary to understand it as it does follow a pattern... admittedly, one it took me 10 years to sort in my mind, but I was very young at the time and the internet hadn't been invented then!
As ever, there were many anomalies with Luftwaffe codes, and only experience will teach you what they are and how to interpret the information you come across. Hope this is of help to you.
Kindest regards,
Paul