I noted you said you were running at 2 knots. That's fast enough for them to track you. I find ordering silent running and then manually dragging the needle on the telegraph and watching until you get to 50 RPM's to be effective when combined with depth. At some point you will slip under the thermal layer [modelled in SH3 Commander although you will not know it for certain, read the notes] and be harder to track. In order to set your E-motors to 50 RPM's you either have to use the mod that allows you to do so from the speed buttons [~] key or use Shift+F2 to free roam through the boat to the chief engineer's gauges and observe the changes made to RPM from dragging the indicator pointer.
50% air left is not the time to panic. If necessary, you can drag it out until you get the "We must surface!" message. I've never been kept under long enough to get to that point, but if I did, I would surface the boat [and die] but then go into SH3 Commander and change my career status to surrendered at sea. It doesn't get you out of your predicament, but it does lend a happier ending to the lives of your Kaleun and crew. There's no way a U-boat crew would try to duke it out with three escorts; they'd be jumping overboard as fast as they could get out.
Also, the fact that they were making "dry" runs on your position tells me they were out of depth charges. From that point on they can't hurt you while you are submerged. Do not give up on evasive action, stay patient, quiet and deep and hope you eventually get away. If you do run out of air, then you must surface and "surrender" your career, perhaps after having made one last desperate attack with your remaining torpedoes. I've found that by running slow, it is always the air that gives out before the batteries, even if I have had to make some fast dashes to escape falling DC's.
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