i had this same problem with my yj. first of all that steering set up sucks. it flexes alot so yu will feel alot of slop in the steering after lifting it. second i would go back to the stock shackles. as said before it will raise the pinion and make the steering do some funky things. i know this first hand when i did my soa, because i pointed my pinion upto the sky and the jeep was ALL OVER THE PLACE. so take the shackles off. as far as the pitman arm goes it will benefit to at least get one from a zj or an xj, so it straightens out the drag link angle a bit and will reduce bump steer..
were any of the bushings on the leaf springs worn out?, were they all nice and snug. check the hub bolts, ball joint bolts, the ball joints themselfs have a habit of wearing out in jeeps.