Improved Kriegsmarine Miscellaneous
I am under the impression that the German Navy's best chance of doing anything lies with 1. better torpedoes and 2. a strategy of dropping magnetic mines from planes and closing out British ports, including Malta.
The strategy would be both affordable given the resources to create u-boats and a surface fleet is many times more expensive, and doable from a technological perspective.
Ultimately it is a hindsight move, you cannot expect old navy guys to start thinking this way. But, it did work against the Japanese in starving their country to death.
The German Admirals thought World War II to break out in the middle 1940s and planned accordingly. We know that the war will break out in 1939 and need to plan accordingly.
Therefore if I was Admiral Raeder I would have taken heed of your second point and built up a much bigger stock of magnetic mines by September 1939.
I would have also followed your first point and made sure that the Kriegsmarine's torpedoes worked. If possible I would also have put more effort into developing faster and more accurate torpedoes, as well as reliable detonators. That is try to get homing torpedoes into service sooner, and if I knew about them, buy a licence to built oxygen driven torpedoes from the Japanese.
Although all the aircraft belonged to the Luftwaffe, torpedo development was the job of the Kriegsmarine and they failed to develop an effective air launched torpedo. The Luftwaffe eventually had to buy torpedoes from the Italians, but that wasn't until 1942. Therefore I would do everything possible to develop an effective air launched torpedo by 1939.
The Luftwaffe's equivalent of RAF Coastal Command was equipped with seaplanes and flying boats at the start of the war which even aircraft like the Anson and Skua made mincemeat of. I would not increase its size, but I would equip all the Kustenfligerstaffeln (literally coastal flying squadrons) with the He 111.
Meanwhile what became Fliegerkorps X consisted of 2 understrength bomber geshwadern, one of which was the first Ju88 unit. The Luftwaffe did not think maritime operations were unimportant, but as Germany was a land power they had to build up an adequate tactical air force to support the Army first. However, if the Germans could build more aircraft before the war (and had Milch been in charge of aircraft production at the time instead of Udet it could have been done) I would use all the extra production to create the largest possible anti-shipping force. Which would be better armed because they had an effective air launched torpedo.
Also Milch might not have cancelled the DB.603 aero engine and allowed Heinkel to re-design Bomber A around it. Therefore the He 277 would have been ready in time to be built instead of the Fw200C.
The Germans started to develop radar 3 years before the British and with a greater sense of urgency I think they could have had search and gunnery sets for use against aircraft and surface ships in large scale service at the start of the war. One way to achieve this is better co-operation between the services so the maximum use of Germany's scientific resources is made. E.g. the Kriegsmarine didn't have PPI for their radar, but they might have if they had known that the Luftwaffe had developed it.