After long time I revisited MS-8 tuning and must say it has made a huge difference. I am not confident of what I have done is right or not but sound boominess is almost gone.
I wanted to do upgrade step by step, laziness has caused gaps between to widened a bit too much now
First I have installed rear sub which was too boomy then installed Jehnert underseats still boominess was there. Even after re-calibration (subsonic 20Hz, JL 12W6 LP 80Hz 12dB/oct, Jehnert 200Hz 24dB/oct, rest all to stock L7 speakers and tweeters) boominess was present. Today I tried to level match (must admit for the first time), only my front door card and underseats are amped. Stock L7 amp and tweeter in rear parcel shelf were too low to reduce amp gain and I couldn't match it to them. Also center channel (powered by MS8, again stock L7 with added tweeter) was too loud (compared to rear) so couldn't level match from front to rear. So decided to level match among front stage, This is what I did:
I reduced MS-8 volume to -22
Played test tone from output identification to the center channel
Measured center using Sound meter
app on my Nexus 7
I had to increase gain on my PDX4.150 almost to 10'o clock position on amp to match door card's speakers with the center.
Then I matched the underseats and for that I had to increase the gain to 12 o'clock position.
After a while I reduced MS-8 volume to like -34 and then checked fronts were still matching but underseats were low, for that I had to increase gain even further to something between 2-3 o'clock position.
Then I recalibrated driver seat. I wasn't getting good feel on such a high gain for the underseats so I reduced it to 12 o'clock position after the calibration.
Sound is better then before, atleast boominess is much low now.
I will keep testing it for few more days and report back if I like it this way.