get an alignment and...
 

...have your tires re-balanced. I know this sounds not worth a post, but I recently had my 11' JKUR (mostly stock) aligned and the tires re-balanced; what a difference; so much more stable and smooth. I have 27k miles on my 11' and I honestly don't think my JK was properly aligned or tires balanced from the factory, it feels better than when it was new. I previously did the bolt replacement and steering shaft replacement and tightened up everything up front, and the alignment and balancing still made a major difference.
I don't blame anyone for saying "Well Navin R you really are a d___ a__ if it took you 27k miles to figure that out!" Well, whatever, maybe someone can benefit from my mistake, I never imagined the factory might not have things set correctly in the beginning, but I think that's the case with my 11'.

I can understand the bolts but why would you replace a steering shaft? Your tires may have been off from the factory. No biggie. Get a measuring tape, a level, and a angle finder and do to making sure everything is aligned.

Where I live, if you get an alignment, by the time you drive home your alignment is out again. NYC roads suck big time.
I don't usually do it unless I start to show signs of uneven wear or vibration.

I have firestone lifetime alignment and rotate and balance. I get it done every 3k miles

Ditto on the Firestone lifetime alignment. I go in 2 times a year get an alignment and request a printout. To me it's worth the 140.00+ I paid. After 3 or 4 alignments and you are basically getting free ones. Every 6k I also have them rotate and balance the tires. (At my expense) i find my JK holds an alignment pretty well, not as long as my Cherokee but not bad. I always go in after pot hole season in New England.

Just to explain; the steering shaft was found to be shot by the dealership and they replaced it some time ago. I just didn't want someone to think the poor driving characteristics I was experiencing were due to a bad steering shaft.