most kits are designed to fit the vehicle with as little modifications as possible; it's what makes them desirable to the average garage builder, they also only have one option for link location, so you basically tied to teh peramitters that the manufacturer specified. Most link suspensions that I have built I have had cut the rear floor up for the upper link mounts so that I can get plenty of vertical seperation at the frame, "kits" do not do this, in turn you end up with less than Ideal center squat, tall ride height, and link mounts that hang lower on the frame.
I've also had to cut off the rear of the frame and re-build it for clearence. I will add though, a lot of this is done based on my design, you can buy a gen right kit and install it and it will be a lot "nicer" than a leaf spring suspension, performance wise, you will get more wheel travel, but durability and reliability become a factor as with any link suspension. re-buildable links will require maitenance often, teh delron bushings will need to be replaced often, as much as every year for a daily driver. if one link fails on the trail, your kinda in a jam. I've installed leaf springs and have left them there for years with out any maintance, I beat the living crap out of them and they rarely let me down. I have bent a couple springs and I have broken one, but I was still able to driver out with bent or broken springs.