Running a DJM 4/6 on mine with control arms up front and a flip kit out back
Coils are said to give a stiffer ride. Depends on who you ask if they consider them to be rough or not, only you can decide that. Spindles will either require larger wheels, or increased turning radius. However, DezertStatic (I think) had a how to on grinding the 16" spindles down so you gain your turning radius back. Control arms will increase bumpsteer, which may or may not be a noticable problem depending on the truck, roads, driver, etc. Some also say that they can not align there truck with them (4"), but they sell upper arms to help get your truck in alignment. With that said, personally my alignment is within in spec.
For the rear, most common is going to be a flip kit. It is easy, keeps towing capacity, and gets the job done. You could also do a 4" leaf and a shackle to get the drop. With drop leafs the ride will increase in stiffness (same as the front will with springs) and loose some of your towing capacity
As for notches, people say belltech is best, then mcgaughys, then djm and the others. Belltech and mcgaughys both wrap the frame where djm and the others are just plates. IMO, with the thickness of the DJM plate I don't see it being weak by any means though.
Popular shocks include monroes, doetsch tech (summit drop shocks), and belltech street performance. I am running qa1 adjustables (more money) and some are running king or fox shocks (even more money).