The best advice I could give anyone about up-dating their factory radio system is to first talk with the folks at Crutchfield. They are a great place to do business with, and they supply you with all the needed wiring harness's free of charge. They are also the only ones that will print you a vehicle specific instalation sheet, that covers YOUR truck and all the little things others leave out. Their prices are very competitive, but if you shop on price alnoe, others are cheaper. I just installed a new system, and decided to go with Crutchfeild, and in the end, I saved money they were lower when everything was tallied up.
For the head unit, you can go with a 1 DIN which is the standard height model you have seen everytime you go to look at car radios. It requires an addapter to fit your truck and looks aftermarket. Dodge, chevy and some fords use the 1. 5 DIN modles in their trucks. it in larger then the standard radio, which allows for more features and larger displays. If you wish to replace your factory radio, with one that is the same size and keeps the look of the factory system, then you too will have to go with the 1. 5 DIN modles like I did. The selection gets narrowed down when you go with this size radio, I choose the Pioneer brand, they have three units in the 1. 5 DIn size to choose from. I went with the P77 model, it has many features and still has the look I wanted. The fit is fantastic, it fills out the factory dash space perfectly and is a snap to install, no spacers, adapters or anything else needed, just bolt it in. Crutchfeild will supply you with all the needed wiring adapters to make the install and hook-up simple, but you will need to decide if you are going to run a seperate amp or not. This is the time to install it if that is in your plans. The front speakers are the easiest to replace, get yourself a door panel removal tool, and it's a snap. To get the best sound, insulate the door and use a speaker baffle. You can choose from the stock 6"x9" speakers or go with 5. 25 or 6. 25 speakers, you will just have to get the right adapters, which crutchfeild will supply. I think component speakers are the best choise for the doors, but thats just me.
In the rear, those speakers are a little harder to get to. They require you to remove several items on each side, but none of them are bad, just more steps. Make sure you have the correct size torx socket, my took a 50. The seat bolts are 13mm, and the screewa are #2.
Good luck on the stereo, The amount of prior planing you do, will directly affect the quality and time of the install.