First the jeep looks great. There is some kind of rattle when I let the clutch out, it sounds like something is hitting. There are some vibrations still even with the mml. I seen somewhere on here to add washers. How many usually. The best of all I didn't have any bolts left over Lmao.
drop the t-case an inch would be the cheap route. You could make your own t-case drop with 1 inch square steel drill holes the the square tubing where to match the bolt holes on the skid and get bolts an inch longer. Or you can buy a one inch tcase drop or do it right (more money though...a good amount to) and get a sye cv driveshaft and adjustable upper control arms.
I plan on a she and cv later down the road as well as a tummy tuck. What needs to be done snug the shifter its hard to get it into 2nd and reverse. Is it simple as a adjustment. I know I need to adjust the 4x4 lever.
I have the same setup...the rattling may be your tcase linkage smacking the body. Or could be something loose/needing adjusted from the install.
I had vibes with the tcase drop...so I left the drop installed when I did the MML. So in your case, install the tcase drop as well. That'll help eliminate the vibes and it'll ride much better. I'd still get the SYE...I think i still have very minor vibes when I accelerate hard and hit around 3k RPM.
For the shifter issues...remove the boot and the foam rubber material around the shifter. Be very careful so you don't crack the plastic ring holding it in place cuz it'll cost you bout $20 to replace it. If you have the rubber boot, you can replace it with a leather boot from the newer TJs and that's sposed to prevent the binding caused by the rubber boots. Other solutions...notch the console or move it back enough that it don't bind anymore. Just a fraction of an inch and then figure out how to secure it. IMO, replacing the boot would be the easiest. I just pulled the trim ring for my rubber boot out, removed the foam rubber around the shifter and tucked the bottom of the boot inside the hole it was covering up. It's not the cleanest install...but I prefer function over looks. I'll install a leather boot when I can spare $30.
"We don't build great brakes because we think you don't know how to drive, we build them for the guy on the road in front of you that doesn't." - Black Magic Brakes
I have the same Zone 3" lift with a 1" MML and 1 1/4" BL and needed to add 5 washers to space down the skid place (maybe 1/4") to get rid of some slight vibes at 60mph. Like suggested above, I believe the sound is from the transfer case linkage knocking which is an easy fix.