So I installed my upper a arms on both sides and had an alignment. I still have knocking and vibrations at 40+ mph.
Do not know what to do at this point.

Thank y'all

Tires, check balance and also for any issues with the tires themselves
Have you checked for any loose parts/ improperly torqued parts?
Have you check the CVs/ front driveshaft rear boot?
Have you checked the rear u-joints ?
I assume you had an issue before ?

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MUDD'S MOTORSPORT'S We do IFS lift installs ,
03 OVERLAND EDITION /Kilby-Skidrow-Mopar-4XGuard skids/ 2.5 inch TOTAL CONTROL JBA coilovers -JBA Arms/MOABS-31 FALKEN WILDPEAK AT3W / 4.10's etc, 04 Kilimanjaro Edition loaded, plus 05 KJ limited

just got her aligned and maxed out on the left front side now while braking at 15 miles an hour horrible grinding noise occurs

the front right side is making thumping and rattling noises at approximately 45 miles an hour plus extremely hard at 55

Pics show rubbing.. wtf is going on? This was supposed to fix my issues from before...
http://www.cardomain.com/usernew/galleries/edit.aspx?id=1152729

Just went to precision tune auto and he showed me where the springs and upper arms are rubbing... how does one fix this. I thought the upper a arms were supposed to fix all the issues with Frankenlift.

Can you post the pics here? Your car domain link didn't work for me. I run OME 927s and 3 ring clevis in front, and I had to rotate the spring on one side to get the arm to fall between the coils at full droop. As far as the shaking and vibration just driving down the road, that sounds like a separate issue.

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2006 Sport 4X4, Deep Beryl Green, NSG370, NV241J, Lifted with OME 927/948 and Bilstein, JBA 4.5 UCA's, Custom 3" Rear Y-Link Extension and Swaybar Relocation, 265/75-16 Toyo Open Country AT2 tires, Black Plastidipped bumpers, flares, and doors, Pioneer speakers, Alpine head unit, 1200w Phoenix Gold Amp, 12" Dayton Reference sub.

won't take us to your section so not sure
plus how high are you sitting now ? If 23 or over then yes you're going to have spring/UCA hitting each other . Have to keep everything 22.5 and lower for no contact
as far as your noises and grinding you're just going to have to track it down looking at CVs , front driveshaft boot, brakes etc

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MUDD'S MOTORSPORT'S We do IFS lift installs ,
03 OVERLAND EDITION /Kilby-Skidrow-Mopar-4XGuard skids/ 2.5 inch TOTAL CONTROL JBA coilovers -JBA Arms/MOABS-31 FALKEN WILDPEAK AT3W / 4.10's etc, 04 Kilimanjaro Edition loaded, plus 05 KJ limited