I just looked up Rustys arm and may have found something.
The stock arms are designed in a way that they can twist a certain amount with out causing any problem. The new Rustys arms are extremely stiff in that sense, the only flex you will get out of the arms is the deflection of the bushing itself. It appears that Rusty is using rubber bushings which is good. If your arms have urethane bushings then that plus the stiff design will kill a lot of travel.
My advise? TEMPORARLY put the stock arms back on and remeasure your travel. See if it improves. My guess is it will, slightly. Then order a set of Good aftermarket Arms and lose the rustys junk. I prefer the design of the Teraflex arm, but RE makes a very good arm too, as does JKS. Either one should get you started.
as for the rear you can build a set of rear leafs that do just about anything you want to do, but it's a lot of trial and error. I just built a set that holds up ALOT of weight and still gives me about 8" of lift. So you should have no problem building a 4-5" leaf pack.
Also in the rear, get a longer shackle the boomerang style is popular, i have a straight design and have not had any drawbacks.
Another thing to check for in the rear is the E-brake cable. usually at around 4" the cable becomes too short. a YJ passenger side (IIRC) e-brake cable is a lot longer and will eliminate the problem.
The rough country are not the softest on the market but you should be fine with them so don't worry about getting new coils.
BTW how long has this suspension been on? They will settle over time and break in, so to speak, and start to ride better and give more travel.
Hope this gives you some help.
Dingo