I'll preface my response with the fact that I've installed replacement head units in many different vehicles over the years. I ALWAYS use Crutchfield as a source for gear and a resource for support. More recently, YouTube is always a big help as well. All that said, I'm not a pro installer. So, first off you need to get the proper gear - that usually means adapters for your specific vehicle including a dash mounting kit. I'd rate this install as being easier than most I've done as far as accessing the area and making any necessary modifications. With the proper "kit" or "gear", you really only need to make 2 small modifications - 1 is just removing 2 bolts and a metal frame that sits behind the factory radio under the dash. The other is trimming about a quarter inch of material off of a plastic rail that runs across the area just above where the radio goes. To do that, I used an electric cutting tool (high speed rotating disc) and it got the job done quick but was probably an example of killing an ant with an elephant gun - in other words it can be done with a small hand saw or possibly even a serrated knife.
Do yourself a favor and search YouTube for installing head unit in JK and you'll find plenty of how-to stuff out there. Same thing for replacing the speakers. I will say that what I found about replacing the dash speakers was highly over-stated with respect to level of difficulty. Watching the videos first definitely helped but it was nowhere near as hard or time consuming as some people said it would be. I had both front speakers out, filled with poly fill and new speakers installed and back in the dash in under an hour.
Crutchfield makes it easy for DIY'ers. You can search for what fits your specific vehicle and they show you exactly what gear you need to purchase with it to make it all work. They even offer a service now where they will prewire your harness for you for a $25 fee so you don't even need to figure out which wires to splice together. And, no, I don't work for Crutchfield but they have certainly received many dollars from me over the years.