I have a 2003 X, 4.0L with a 4" suspension, 1" BL, MML, Tummy Tuck. I ran a 1.5" T-Case drop and I did not think I had vibes either, but when I added the sye / ds, all I could say was wow, It drove like a brand new Jeep. I had vibrations before but didn't realize it.
I added the MML after the sye / ds was installed, so I can't say if it will work or not. But if it were me, I would add the MML anyway, and ditch the t-case drop and see how it rides. If that doesn't work, you could add smaller spacers for the t-case drop. You will more then likely need sye / ds / adj uppers to get it super smooth.
I have a 1" Brown Dog MML with rubber mounts. Wicked good quality.