Ride quality - I just want to make a suggestion - you're not actually comparing the OME ride quality to stock, you're comparing it to the ride you had with the original dead sagging stock springs.
Many of the ride quality complaints with OME gear can be traced back to an incorrect selection of springs, the medium springs you have chosen indicate that they are suited to carry the vehicle manufacturers full design loading plus an additional 100~175 lbs - if you have less load than this (say a driver alone), you will have an excessively rough ride.
The second area of consideration will be your tires & tire pressures - if you're running an LT tire, chances are the sidewalls are excessively stiff, and given the light weight of the Samurai, they will not be as compliant as they could/should.
I'm not going to suggest that you shouldn't modify your vehicle to suit your needs, but I need you to understand than the manufacturer chose specific OE components, and the more you deviate from OE spec, the bigger the impact of your modifications - you need to understand how the modifications affect the vehicle and then decide if you can accept the compromise.
One of the Suzukis I have here has had the suspension tweaked and tuned - poly bushes, sport springs, larger sway bars, larger disks & calipers - it now corners like it is on rails and can outbrake many a more expensive, high performance, sports car, but I no longer drive it (my son does, and his sister loves it), I find the ride bone jarring - oh - I forgot - it also has Recaro sport seats, which are THE most comfortable seats I have sat in, but they don't compensate for the ride