The shocks are all around pretty good, especially for the price. I constantly have cargo back there and also towed with them, and they were firm, but not stiff. They also keep the back end from sagging too much. Plus, if you need new shocks anyway, you might as well replace them with these.
Shackles will not have an impact on the ride quality. They just drop the back spring mount to provide the lift. Shackles will not bend your spring to return them to the stock height. The spring will have less arc to it than with the stock shackles, but it will still be lifted a few inches.
The add-a-leaf kit is usually cheaper, and those extra leaf springs will make your ride more stiff than stock. They also require a little more work to install, but nothing too intense. You'll need to add a spring to the leaf pack, where a shackle lift is literally taking out 4 bolts and putting the new ones in.
I'd recommend doing the shocks plus shackles first. Then do a TT enough to level out the front and rear. You might have to get some camber bolts for the upper control arms to get your wheels aligned again after the TT though. If you still have running boards, take those off. Those things take up a few inches of clearance on the bottom. If you still want more lift later on, you can always do the add-a-leaf and crank the t-bars more.
EDIT: If you haven't already, look through this thread to see what lifts and tires other people have run, and compare that to what you want.
http://www.explorerforum.com/forums/index.php?threads/show-off-your-lifted-2nd-gen.145744/
EDIT 2: You can also replace your 2-door Sport springs in the rear with some 4-door springs to get some lift. The 4-door springs are designed to hold up the extra weight of the 4-door vs 2-door, so it will bring you up a bit. You can probably find a ton of 4-door springs in decent shape if you have junk yards close to you.
