If you're only going 3" and mostly road driving, then I wouldn't bother with the longer radius arms. If you go to a 6" lift then definitely get the longer radius arms becuase that tells me you'll want the longer arm travel when offroad.
You can also save money on the leaf springs, I dont think you'll need them. Just get belltech shackles and call it good. That shoudl save you a good chunk of change. If you were going higher than 3", like say 6", then I'd probably recommend the new leafs to help reduce the amount of blocks you'd have to add after you max out the belltech shackles. Belltech's will give you about 1-2" in the rear, which is perfect to level out the truck if you're lifting the front 3".
You could use 4" Skyjacker coils, sure, but Im not sure how much the James Duff brackets drop your pivots... probably not as much as the 4" Skyjacker ones, almost definately not if you consider the 6" holes that are there on the same bracket...
James Duff brackets will drop your radius arms and pivot beams down exactly 2". On my supercab 4x4 I think I could easily go with 4" coils and it would be perfect, maybe still need 1/2" of spacer to get the geometry just right. In fact, I'm thinking at some point I will swap out the stack of washers and JD coils I have for some skyjacker 4" coils at some point.
I will say that I LOVE the ride of the JD shocks and coils I do have. It really soaks up the bumps in the road with ease. Compared to the procomp shocks I have in the rear, its a night and day difference. The procomps really make me feel every slightest bump I hit in the road. Swapping in a pair of JD shocks in the rear are also in my plans.
I've heard nothing but praise for the SJ stuff, but I still don't know why they drop the drivers side pivot arm an extra inch or so lower than the passenger side.... the JD drops both the same amount.....which makes both sides alignable to the same extent
Since you have no desire to go 6" then I'd recommend the JD kit and if its not enough or you dont like the coils, then swap in some SJ 4" coils later.