Let me start by saying I have never installed a lift on a vehicle before. I have been looking at the Liberty Lift FAQ but I still have some things I want to clear up.

First and foremost, is there a lift that includes everything I need (bump stops, top plate, etc.)?
What tools will I need for this?
I have to replace my shocks regardless, does anyone have a working link or part number for the right shock to do this job? www.jeepinbyal.com or http://www.boulderbars.com

2.5 inch seems to be the ideal lift height, what specific tires (most time will be DD, but I would like good traction off-road as well) would you recommend after installing this lift?
If 2.5 inches then you will not need top plates/clevis etc as the OME 927/948 combo gives you 2.5 inches with nothing else added. as far as tires 245-70-16s or with few tweaks 245-75-16s / 265-70-16s ( same height ) but will lose power and mileage .

Is a 2.5 inch lift going to make a noticeable difference as far as ground clearance or is the main benefit bigger tires?
Yes it will, I will post a picture with a 2.5 inch lift

Are hockey pucks reliable for bump stops, and why would OME not need bump stops?
All lifts need bumpstops so you don't go to far up into the wheelwell and tear up your tires and over compress your shocks, yes hockey pucks work great in the rear, that all I use here on lifts.

Being a 2003 I shouldn't have to adjust the brake line, but are there any other modifications I might need to do? Not really

Adding bigger tires would require me to adjust my speedometer, how would I go about doing that?
Pinion reset at dealer

What would be the best place to get undercarriage armor for my KJ?
Kilby if they still have gas tank skids or above jeepinbyal has great skids

I'm leaning towards buying the OME lift but I'm concerned that I won't be getting everything I need to do the job.
If anybody happens to have links to the items I will need to purchase I would greatly appreciate it.
you need 4 springs 927 front / 948 rear , then look on the JBA website for either OME or Bilstein front shocks and 2.5 inch lifted Bilstein for the rear

Thank you for all your help.

Now if you want to go ultimate be ready to spend a little more and get the JBA coilovers, fantastic ride and handling both on and off road
There is also a tommudd Econo kit that has springs/ shocks/ JBA UCAs etc for a 3.5 inch lift just have to add bumpstops Teraflex for the front and hockey pucks for the rear

Thank you, I appreciate all this knowledge you have shared with me! Where would I go for the tommudd Econo kit? And would I have to make any adjustments going into the 3.5 inch lift? You also said hockey pucks work great in the rear, what would you recommend for the front? Teraflex?

Thank you, I appreciate all this knowledge you have shared with me! Where would I go for the tommudd Econo kit? And would I have to make any adjustments going into the 3.5 inch lift? You also said hockey pucks work great in the rear, what would you recommend for the front? Teraflex?

everything you need is right here http://jeepinbyal.com/liberty-2002-2007-kj.html

except for the hockey pucks. you can get those from amazon.