as mentioned a few times....the harshness you are feeling, based on how you've described it, is probably related to coil stiffness. EVERYTHING I am about to type is related to your last sentence saying that you are trying to learn about suspensions, and is my feeble attempt to answer your questions
Slight changes in handling, however, can be attributed to you lifting the Jeep which in turn changes the geometry of all of your steering and suspension components. Depending on how high you lift your Jeep, there will be different routes that you can go to correct these changes and return your handling to a closer to stock feel. Examples of this would be adjustable control arms, drag link flip, axle side raised track bar bracket
What about the rear feeling different from the front?
I feel like the rear just goes over things weird. I am not sure if this is just a lifted characteristic of my jeep that I need to get used to or what.
When you buy a kit, you are truly at the mercy of the manufacturers choice in coil spring rates. This goes for EVERY kit company out there. If you run a crazy heavy Jeep with huge aftermarket rear bumper, carrier, jerry cans full of liquid, heavy spare ire and rim, roof rack and a ton of gear in the back, etc...then a soft coil will probably not be best for your daily or regular uses. The coils that you have sound like they are a heavy spring rate which is causing the(what I will assume to be a) lighter rear of your jeep to ride harsher than your heavier front where the engine rests. The only way to make your Jeep handle "like stock", after lifting and adding heavy aftermarket mods, would be to get a custom coil rate that completely fits your new lift and Jeep weight.........Long story short, you'll have to learn to deal with the new feel OR buy a softer spring rate to make your jeep ride more smoothly!
Can these weird feeling results come from the stock rear control arms
no. Having stock control arms will keep the ride "harshness" the same as stock. Not having the correct control arm lengths CAN cause drive line vibrations and/or poor handling at higher speeds and/or flighty feeling of the steering wheel .
or can the sway bar links being short cause a weird sensation in the rear while turning?
no. the only thing that effects your "feel" while going around turns at higher speeds is the sway bar itself. If you want your vehicle to ride smooth while going down the road, then you want a softer sway bar. If you want it to corner like a corvette, then you'll want a more firm sway bar. That being said, I have NEVER seen someone buy a heavier or more thin swaybar in a Jeep and usually only is done on larger and heavier vehicles like RV's or trucks used to tow.
Should I loosen axle side of control arms in the rear with the weight of the vehicle and re-tighten just to be sure they are sitting right? Thanks
This has nothing to do with what you are feeling BUT...Any time you lift a Jeep, you should have it on the ground and at ride eight before you tighten your control arm and track bar bolts. This will assure that there's no binding or stress on the bushings once the Jeep is on the ground.
Another question about the sway bars. I thought they would give harsh ride when hitting bumps that don't cause suspension to move at same time right to left. So if I hit a hard bump on one side it would be more harsh relative to sway bar stiffness. The example I always heard was hitting a speed bump would not but a pot hole would. Just trying to learn some things about jeep suspension. Thanks
This is not true. You are driving a sold axle vehicle. Any time you hit a bump going down the road, you will have shifting of the complete axle from right to left(or vice versa) depending on the severity of the bump or pot hole. upwards compression of the entire axle(like going over a speed bump) will shift the entire axle to the passenger side of the Jeep. A hole causing the entire axle to drop will cause the axle to shift to the drivers side of the Jeep. None of this has anything to do with your swaybar links OR coils. In this particular situation your coils will only change the harshness or severity that these changes occur.