I think most of the shocks that come included with a lift kit are not the greatest quality( make for a stiff ride)
I bought a 3.5" lift from rubicon express and the included shocks made it ride like a Suzuki samuri (very hard)
replaced the shocks and made a world of difference best money I ever spend. I took it out on the rocks today and it flexes beautifully am very happy with that. Just have to retain the front springs they come of the seats when it really flexes.
For the front, its rather easy with some coil hold downs from an XJ. Some earlier TJs come with one side coil (passenger) hold down. The driver's side has a hole in the lower coil mount, but no hold down.
For the rear, its a little more critical as well as harder. You could drill a hole in the middle of the lower mount and use a piece of flat plate. Simple and effective. This hole is also where you put your bump stop extenders. The rear axle has plenty of room to get a bolt and nut together there. The front axle on the driver's side only, whereas the passenger side has the track bar mount limiting the access to get a bolt and nut screwed together.