Put the new UCA's(stock) in and transferred the new ball joints from my old blown out LCA's to my new/old LCA's. Reamed out the LCA slots to match the Cam Bolts, so hopefully, now it will align. On a side note, the drive home was the quietest I can remeber other than the front tires roaring from being out of alignment. The only noise I heard on the bumps and the washboard road coming home was the Fox's chirp on sharp jolts. Now if my rear 3.0s would show up all will be rainbows and unicorns.
For those dealing with the clunk. Just replace everything and get it over with. Though with all the practice doing the front end, I'm now pit crew fast on changing crap out.
UPDATE: It all aligned. Woo Hoo. It feels a little stiffer in the front now, though, because of the new UCA's but I'm sure it'll soften up when they break in.