Wow, that's a lot of questions

Let's see...
Safe distance from target: OM is quite forgiving, but still, 3000m is a very very short distance. I'd keep the target almost touching the horizon, barely visible. And since they're more likely to spot you as you move ahead of them, I usually keep them out of view and check where they are with the hydrophone (manually). WHen you turn parallel to your target, you'll hear a guy say "Aye aye captain, new course XXX". You can maneuver as you want and then get parallel just by entering that course again. And you have the message box just in case you forget it.
Turning 90 degrees: why would you need the TDC for that? If you're on a parallel course, just turn 90 degrees into the target, simple as that. As I said, it's better to refine the AOB solution as the target gets close, nut just rely on a "10km away 5 second estimation" for the entire attack.
Plotting: again, why would you need that? But anyway.... True Bearing = Bearing + Sub's course. You extend a true bearing line from your sub and stop it at the estimated range. Then you use the protractor to create an angle equal to the estimated AOB between that line and the target's course.
Speed: as I already said... stop the sub. There's absolutely no benefit in pointing your sub at the target. You should already be way ahead of the target so you should have time to do that. However, the target's AOB must be at least 45 so you can get a clear view. Or, calculate the speed when it crosses your 045 or 315 bearing. In that case add your speed to what you calculate.
Torpedoes: never ever use electric torpedoes with magnetic detonators. Not until late in the war. They're still way better then the ones we had in SH3, but an electric torpedo with an impact detonator will always do the job.
The small numbers at the center of the AOB dial: arre you sure you've read MY tutorial? Because in that case you'd know they're just numbers of the periscope lines, or "milirads" as I like to call them. While the main reticule had 1 tick every 2 miliradians (the 5'th tick being numbered "10"), the AOB wheel has one tick for each miliradian.
English labels: They're included as an optional in OMEGU, just enable as you would do with any mod.
Autoupdate Button on Attack Map: It does the same thing as clicking the one on the Periscope Screen. The only problem is that if you click it once and then leave the screen, the "blue lit, unlit" behavior of the one on the Attack Periscope will invert. It's just a graphical error and nothing I can fix. All dials work the same way. And yes, even in the Attack Map screen you still need to put Autoupdate OFF to enter data into the TDC.