I have done three runs through a scenario with the Sen Toku, 3 different versions of the game, but I only use mods from within the mod itself for the first two runs, and none on the last (recommended). I also cleaned the Save folder prior to playing the game. I don't know where you're game is failing, but here is a blending of the three runs:
Patrolling in the Volcano Island Group when an Ultra / Magic message comes across:
Sure enough, there they are:
The first run-through, I shot all six bow tubes at 'er, missing with just one (somehow). Missed behind with the last one. The sub was visibly sinking before the 2nd one hit. I did not take pix, figuring I would video instead, which failed miserably... I am turning into an old tech fahrt that can't keep up with today's "easy" tech stuff... ah well.
The 2nd run, two shot, two hit, and I had turned duds off. She never saw 'em coming until too late, because I managed to close to within 1000 yds.
Making like a submersible, but with some help
The 3rd run was done with manual targeting, so I shot a 3 torp spread. First hit a little behind the conn, #2 missed behing, and #3 barely caught the stern, but the boat was sinking by the stern after just the first hit.
I never did encounter any return fire from the Sen Toku, though I am certain that if I would have been out in front of them, they would certainly have sent some fish my way. As it was, the only torps seen on the attack map were mine.
sub sunk and mission completed.
So, the sub is actually a pinch too delicate. Check your mods, removing them all and restoring one at a time until you find the offender. If you hadn't deleted the Save folder, do so. Although you will lose your career progress.