good questions. let me just leap your frog
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1) the escort carrier is assigned to the troop transports, that's right. the CAg will help keep the transports safe (I hope), along with some screens.
2) yeah. we are going to go carrier route. however, until we can get enough of them build to take over, we will need those battleships and battlecruisers to keep our shores safe from those savages from across the Channel, so until now we've researched everything we could, because we can never build enough ships to overcome the Royal Navy. this way, the excellence of our officer training regime will keep us alive at sea. (actually, for those of you interested, the 4 combat fleets of Plan Z ARE a workable option in HOI3 on normal by 1940, but that would mean sacrificing army and air units, which I don't really want to do in a tutorial AAR).
3) and 4) these two cancel each other out, so its in our best interest to keep them at the same level and then leave them alone. RL Fighter Command definitely favored Bomber Targeting: they never went into battle during the Battle of Britain if there were no bombers around. But we are playing Germany, and as an offensive-type of nation, we need to be able to take out the fighters as well as the bombers. As for the other two, my personal preference is Forward Air Control, but, again, you never know what you will find during war. So put them on an even keel and forget about them.
5) radar. I always try to have 10 radar in Wilhelmshaven by the time I invade the Low Countries, as they will allow me to keep a close eye on whatever the Allies are doing behind the begian border, where we can't see them. If you can spare the IC (given that they're cheap), at least 2 in Dortmund and leipzig. maybe Köln. those are the AI's favorite targets. having them there makes it easier on our fighters to ward off enemy bombers.
6) the only option here, is to sacrifice as much as you can. there's a lot of 1938 tech around, but less 1939 tech. we will gradually move points over from one thing to the next. worst case scenario, transfer all LS to officer training for a few weeks. it really doesn't take long to build it back up to 100+ %. and we have the Sitzkrieg, where we will be doing our upgrades, giving us about 6 months to get back on top.
interesting suggestion regarding resources. I may do that.
edited to add: radar lvl-10 in Wilhelsmhaven also allows us to keep an eye all the way to Dover and Home Fleet. later, by 1941, lvl-10 in Köningsberg comes in handy.