I have this lift, I have 33" tires. I tore my boot on my front driveshaft. I'm lucky I changed them when I did because they were complete crap when I changed them after having the lift on for about 9 months (tore the boot around 7 months. A 2 door will mess up your driveshaft quicker than a 4door because the lift screws up the angle that much faster. I can't say much to what is making this noise right now since your boot is not torn...
But my suggestion is you will need a new front drive shaft, rear drive shaft and control arms... I went with front lower and rear upper to get my pinion angle back to an appropriate angle... At first I just did front LCA's but since the angle was messed up and with a double u joint driveshaft I was getting vibrations at 25mph-40mph...
I went with Tom Woods 1310 shafts and some Teraflex front LCA, rear UCA to fix this problem. If you didn't find out already you should have had to replace your stock front track bar with the lift too, if not you are probably driving crooked like I did for .5 mile until I rechecked everything.
Your 2.5" lift will very quickly turn into a frankinlift like mine if you want to get things correct. I am probably ditching the Pro Comp Shocks and getting Bilstein's and front adjustable UCA's to fine tune my Caster Angle. The rear shocks are too short and about to blow at any point and I have a little more float on the highway than I wish. All I am going to be left with from that lift will be the springs, rear track bar bracket and bump stops.
Just my experience with a similar set up, so take what you want from it.
2010 2dr Wrangler
2.5" ProComp Lift, Front Adj Trackbar, JKS Disco's
Tera Front Lower Controls Arms, Rear Upper Control Arms, Synergy HD Balljoints
Tom Woods 1310 Driveshafts
33" KM2's on ProComp 7069 16x8's
AEV Premium Front Bumper, IPF 900XSD Lights, Warn 9.5ti w/ Synthetic Line
AEV Rear Bumper, Tuffy Security Deck
D30 Front Sleeved and Gusseted, RCV's, ARB Locked
4.88 G2 Gears
D44 Rear ARB Locked, Chromoly Shafts