Welcome back Cultist.
Firstly I would ask why, if you adjust the range to 3000 anyway you don't just set the correct range from the start? when shooting at 500 - 1000m it shouldn't make much difference PROVIDED all your other settings are correct. If you set the range upto 2500m further than the target actually is, and then mis-diagnose the speed of the target then even at this short range the eel could miss. The results will be more marked the faster the target is travelling.
As you progress through the war you'll be forced to take longer and longer shots to avoid detection so get used to getting the correct range now!
Secondly I agree with you that prolonged bad weather is a PITA. In this type of weather I would recommend staying submerged (at least 30m down) at ahead slow (about 2 Kts) until your battery is down to around 80% charge, then surface to recharge fully then down again. Below 30m you'll still be able to
hear upto 30 Km away rather than
see upto 500m. By not letting the battery dicharge too much you'll minimise the amount of time on the surface and give youself the best chance of detecvting the enemy.
This isn't as fuel efficient as running on the surface constantly but it's better than ramming a destroyer in the middle of a storm.
steve.