@Pax. Firstly, thanks for the refining questions. I decided to post less information in order to bring out more details I could be overlooking. It goes without saying these bonus training skills I dont focus on heavily. It is something they pick up on as time passes when they find themselves less active. Noted about the Air skill. I guess that bit of extra training they grabbed, as you said, increased their Def skill enough to make them that much *tougher*. Secondly, let me try my best to answer your queries.
So, the first question is: What altitude do you fly your patrol missions? That will answer your NavB or LowNav questions. I tend to fly my NavS missions from 4K-> 15K. I tend to fly my ASW mission 2K - 4K. I rarely train up pilots in both NavS and ASW because it takes too long to get proficient in both, I need these pilots too much to wait, and I never use Emily in ASW. Get so few patrol groups, I would never waste them on ASW. I only use FP groups on ASW along with lots of them on NavS."
The large majority of my ASW missions are run at 2k-5k. Search missions are usually run at 5k-10k. The Alt of my missions is determined both by how few planes I have to run in this area ( I run lower Alt for better results or so it appears) and by how many military ships I expect to see in the area. If the answer is almost no military ships or air bases in the area to be covered I tend to run lower altitudes. If I know these few planes need to search best they can and dont really have the numbers, I run lower altitudes. With the above said, when setting their initial orders, my first impulse is always 2k for ASW and 5k for search. I then evaluate their conditions and adjust.
I dont find the FPs that difficult to train for both ASW and NavSearch but, then I am no expert and not playing against human opponents! I manage this by doing the initial squadron expansions via the Chitose and then set some for ASW and some for Search. They then swap once reaching 60ish. It should be noted the initial expanded float planes squadrons are hard to fill ( as you know) so I press the best of these into immediate Searching around Takao/Pescadores then adjust from there. Your thoughts on this make me consider some training adjustments here. Does this mean you are essentially running in the same zone one squadron at ASW and one at NavSearch ?
As for the NavB and LowNav this brings up my question again. Are these a factor in success or is the ASW and/or NavSearch mission wholly reliant upon that skill alone?
Final answer/comment: I suppose it is rather risky using PAs for torpedo runs. I use this on a very limited basis and dont consider this a primary function. Consider it more of a gap filler. it could also be said I shouldn't allow this gap to occur... hrmm....As for ASW on the PAs, this again isnt a regular thing but more of a gap filler. Hrmm... See my previous comment

I use the training time in these two skills to raise the PA experience. As we all know, better exp and morale pilots tend to race out to their planes and are ready to fly almost as soon as their orders are given
@ RangerJoe and Pax same time. So you find the Jakes are sufficiently usable in the NavB role that I should look into that? Wouldn't this mean increasing Jake production as well? I do increase this normally but, only in small amounts. Plenty of other resources being spent on research for other planes. Using Jakes I have seen in AARs. I guess I never really considered it much due to their bomb sizes.
Follow-up question: Do you find it better overall doing search arcs as random or do you finely tune and customize ALL search squadrons? I used refined arcs only in certain troubled areas.
"edited for clarity and corrections"
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