You should first try backing-off Webster's Ship Maneuvering Fix. The mod was built basically for Stock ships, and TMO has a few more ships, and the other ships have been changed. Since the Maneuvering Fix is applied to the ships themselves, you're actually overwriting part of the TMO changes.
Another thing to remember is TMO itself is a difficulty mod, and as such, the enemy AI is bumped up, such that they "hear" better and can see periscopes from further out & more quickly. Things like the effect of thermal layers have also been lowered. Ahead one third is too loud in a lot of situations, especially on approach when passing near / under the lead DD. You could use the alternate speed dial, with the "knots" and set your boat on like 1-2 knots, while under silent running, and minimize your "sonar footprint", being about 40-45 foot below the thermal layer. Even still, they might hear you. You leave the shears above the layer, or go too deep under the thermal layer, and you will be heard in TMO. If you get really curious about individual ships' sonic abilities, you can look in each of the ships' folders in the Data / Sea folder, under the ship's name dot SNS file, and see if they have a "Sensor X" section with either an "H0x" (hydrophone) or an "N0x" (Sonar) in their list. The 'X' and 'x' stand for a number, such as '1'. It is a text file. Of course, sometimes finding a particular ship in the folder structure can be a bother...
