Are you running new drive shafts than you could at 90mph. could just be a balance issue on a drive shaft. Did you break in the gears properly? My advise is to take it to the best driveline shop in your area and get their assessment, probably not a 4x4 shop, think where a guy with a street racer would go. Gearing is not really a good diy area to install let along diagnose unless you have a lot of experience with replacing drivelines. Without feeling or seeing it, it is gonna be hard to get a real fix since there are multiple variables involved. You are gonna want at least front lower adjustable arms if a 3.5 rubicon super flex is 3.5 inches of lift or more.
2011 Jk 2 door 6 speed. 5.13 gears, 1350 driveshafts, cooper sst+ 35s, warn 9.5, various armor, 1/4 pounder bumper, 12 inch King coil overs, CB, still running the dana 30 sleeved and gusseted up front. Someday wanna go with 1 ton axels but for now I love my JK.