I had a similar problem with a MIM Jazz a few months back and yes I was looking for that perfect reggae tone, I tried a few different pickups but and different flatwound strings and I came to the conclusion that the bass itself just didnt have the deep tones "in the wood" that I was looking for. Even with an Audere preamp I couldnt get the tone I wanted. Though it was one of the best feeling basses I have owned. I decided to end my quest and I put the Audere on an SX 5 string Jazz with some chromes and now I more or less have what I want.
I think the MIM was just too bright sounding to begin with and nothing could change it. Try playing your MIA and MIM unplugged and listen/feel the vibrations in the body I bet you will notice a big difference