My reply came out rougher than I expected, accept my apologies.
I agree with you, a Kaleun's main job is targetting convoys and big ships, especially transport ships and tankers. If I decide not to do so presented with an occasion my main decision-making factor is that, were it real life and I had to submit my KTB after this patrol, I'd need to have damn good reasons and justifications for that decision backed by both practical experience, precedents, and the Submarine Handbook. For example, should Donitz himself or one of his staff officers ask me why I did not pursue such-and-such convoy, I'd say that the convoy was too far away according to my position and calculations, the sea and winds were too rough, stormy weather, etc. Such reasons would be found in both my KTB and in the Navigator's own log (like weather information, calculation of distance and ETA, etc).
However, should at least some conditions are favourable it is my duty to try to make visual contact with the convoy and report to BdU. If I miss the convoy but can prove I've done my utmost to try finding it, my take is that Donitz would not hold it against me. However, if I attack I must be relentless - if conditions allow I must attempt to reengage the convoy.
Targets over 5 000 GRT are considered good targets. My rule of thumb is one torpedo for each additional 3000-5000 GRT (so 8-10K GRT = 2 eels). Targets of opportunity under that tonnage warrant either a single torpedo (hit or miss) or the deck gun (if not armed) if weather and conditions render an attack practicable. However, if a target is damaged I must continue until I sink it unless it would be unreasonable to do so.
Finally, I stay in the patrol grid area until ordered to a new grid or my fuel reserves approach the lowest estimation that allow to return home, plus 10%. I also expand my search pattern to immediate neighboring grids if, no contact has been made after 7-10 days. However, I try never to go full rogue unless I receive operation freedom, and even then I go to the closest grid with convoy routes nearby.
BTW I have just started my first career with 100% realism, Full Nav, and Enigma messages on. I took your counsel and started writing my first KTB (positions, weather, course and corrections, etc.)