Yes, way to go on opening her up!

Another possibility is when the amp was installed at the dealer they mistakenly flashed the HU to include an Amp as they would when installing one of there Boom amps. Uniformly the only way to tell is to have the dealer hook the bike up to there computer and take a look. Withe the BT355 Line Levelers installed it should be set to stock, with NO amp installed, rear output and fade enabled.

And out of curiosity take a look at the adjustments on the Line Levelers and see if they are set to default before making any changes.

Here are a couple of pics of the default settings.

 

I have not heard of any redesign of the BT amps that eliminates the LL, It would be silly for them to do that, when the same amp is used for all year bikes. And the 14 and up are the only ones that need the LL, I am afraid you misunderstood something....

 

YES,, check to make sure they are at default,, don't ask me how I know,, well, go ahead, ask if you want.....

 

The very reason I brought it up.

 

clackavosticus you said you have your bass set in the middle, did you try turning it down a couple segments? I have mine two to three segments to the left of center.
The speakers need to break in.
Is the issue with bike running or not running? When bike is running you will loose some of the "richness" of the sound. Which in turn takes some bass with it. You should also "tune" it with bike running.
Just a few thoughts.
Hopefully the dealer didn't mess with the settings on the line levelers, Jim has a good point there.
And if they did Bert's pictures of the line levelers will help.

 

Well I hate to say it but there's a chance the breakout harness is not wired properly myself and Greatsteaks had an issue similar to yours.
I would definitely call Bill at biketronics and explain to him what your system sounds like he is aware there was an issue with the breakout harness not being wired properly
Have you faded from front to rear to see if you can notice a difference in sound quality?

 

If the breakout harness is faulty what symptoms should the fade between back and front sound like - the same? - different?

 

On mine and I think Greatsteaks our front channels were out of polarity, meaning the + & - wires was crossed wired. the rear channel sounded fine.
Fade from front to rear to see if you notice a difference..
It may not be your problem, but we just went through this.

 

Does the BOH connection to the HU look like this (stock connection) with the pin numbers on it?