Differences in Line Output Converters

Sounds like a clipped signal.  Is the deck volume ever over the halfway mark?  Did you find the clipping point on the stock deck and use that level to set the amp gain (thus my reference to the halfway mark)?  What amp are you using to power the L5?

With LOC's, I know there are audible differences between brands/models of high quality LOC's, and that's with the benefit of adjusting for voltage input.  A cheap converter uses cheap components and is set to a standard ratio.  I like the Navone converters.  But your problem may very well lie somewhere else.

The amp will have only one adjustment for gain per channel.  It's probably labelled "input sensitivity" or something of the like.  What you described are the choices in crossover settings.

The high level input built into an amp is generally same as a cheap aftermarket unit.  Continue to leave it out of the picture and move up to a high quality converter.

Volume levels cannot be low for setting gains.  You can find several good descriptive posts on proper gain setting HERE.  I have written some of those myself and you'll find some that include an LOC in the description.  Test tones are crucial for this and you'll find links for those as well.

The manual for the MRD-M300 mono amp is online HERE.  Gain should be mode 1, input mode.

This depends on the LOC that is used. If you are feeding too "hot" of a signal into the LOC and it was not designed for it, this will manifest itself as a problem with levels. I hate basic LOC's, even brand name ones. They generally do a piss poor job of signal matching for the most part and unless you pay the man for a premium one, you cannot use them with the majority of amplified systems as they cannot take the increase in input signal. If you have a LOC that has a adjustment to the input and output sections, this is great, provided that the LOC can take the "hot" signal coming in. My advice is to ditch the LOC all together. Use the Audio Control LC6 + bass remote and save your money, use ING Direct....make that it will allow you to use your system properly in a manner that you cannot use it right now. It is a highly advanced LOC that will give you a signal input of any type, high or low level, a line driver (something that basic LOC's do not have), a noise killer circuit (another thing that most LOC's do not have), a remote on output trigger (yet another thing that most LOC's do not have), gives a front / rear / subwoofer preout for future expansion (buy additional LOC's to do the same) + it finally adds a dash mounted indipendent level control strictly for the sub (another thing a LOC does not have). This allows you to tailer the sub to the specific song you are playing indipendent of the master volume control with no more adjusting the bass control on the deck to try and compensate.

www.audiocontrol.com