Hello again!
You might have noticed that unlike modern nuclear subs, WWII subs are more like surface vessels with ability to dive,for a relatively short period of time. They are submersibles, not actual submarines. Later snorkel helps in this regard, but still. They are also slower under the surface. Not just for the speed, you have to be as much on the surface as possible to keep batteries charged, air tanks full and CO2 levels low etc. so you are in best possible situation to sneak away when destroyer is pinging you and you just can't surface.
Your speed in surface can be 16-17 at ahead flank. If your target merchant is really going 25knots

and zig zag, it cannot and won't be doing that for long. If it thinks it lost you (and cannot detect you anymore) eventually it will return to it's original course (before it saw you) and slow down to cruise speed maybe 6-10 knots. So take some distance and follow target with your hydrophone for a while. When target returns to normal routine, make a new attempt to get to the firing position.
Also, I would not be worried with your engine sound when there are only merchants. They can't hear you. But they can see your scope and if you move too fast while your scope is up, they can spot its wake.
When surfaced, your ships silhouette is so low that you should see enemy well before they can see you, especially when boat is facing straight to the target. Also usefull is Decks awash command, that applied you leave only conning tower above surface. But you lose then much of your speed.
Check the awesome four bearings mehod by Kuikueg if haven't already for more professional and pecise operation with distant targets.
And here is really tons of cool stuff, manuals, patrol reports etc.:
http://www.hnsa.org/doc/index.htm
Good luck and happy hunting!