I'm sure you are aware of this thread :
http://www.subsim.com/radioroom/showthread.php?t=172432
It changed my life. Before, I was using LRT with some tweaking of mine, essentialy to keep the fatigue model on.
Now, I just have changed this few lines in the basic.cfg file :
NumberOfCrew5=10
Interval1_5=5.1
Interval2_5=1000;6.5
Interval3_5=1400;13.7
It gives me realistic repair times, many hours for heavy damaged equipment, no influence on crew efficiency in the other Uboat's compartments, no influence on fatigue model, and flooding recovery times that seem to be realistic too, 20mn for a 1% hull damage.