I've pretty much done this on my gen 3 at this point. The tweeters in the dash are the biggest problem though as they are somewhat uniquely designed to have the mounting plate integrated with the speaker. It's very hard to find an aftermarket tweeter small enough to fit in the hole and still have it point at you.
That being said, I went for the "factory fit" approach as much as possible. By that I mean I picked stuff that would fit in the factory positions under factory covers, so it might not be the highest quality stuff I can find, but it certainly sounds better than the junk full aftermarket setup that was in my car when I bought it. The tweeters were Kicker KS150s or something like that. I think I still have the box downstairs somewhere. I modified them to cut the case off and mounted them using a ***** hole they had in the back and made a metal plate to ***** them to on either side. Now that I have a 3D printer I would probably look at doing something with it to make a better mounting setup. The door speakers are something like Kicker KSC650s (they are just the older model, don't recall the exact part number off the top of my head). The Viper is unique in that it doesn't use the typical 6.75" round speakers, it uses a 3 hole 6/6.5" design. Looking at the design I think you'd have to cut the little tabs off that are there for the 6.75" mounting, but mine didn't have that at the time. I waffled between cutting the tweeter connections on the door speakers and not. Theoretically you don't need them since the dash ones should be doing that work, and I wasn't sure how the small passive crossover on the speakers might mess with the other crossovers I had in the car. I used a Kicker 6.75 CompRT slim subwoofer in the factory box for the sub. My car didn't have a factory amp originally, so I had replaced it with an Alpine MRP-F300 that fit under the passenger seat in the same spot with a random set of crossovers that were in the car when I bought it. I fought and fought with this setup and tried tuning it a but of different ways, but never really got anything super great. It wasn't bad, but honestly, the factory system in the 03 my dad had for a while sounded more powerful to me, so I'm not sure why people give them so much grief other than maybe being a bit fragile. I also had an Alpine CDE-HT137BT head unit.
Since then I've swapped over to a factory RB1 head unit for the nav and managed to find a factory amp. I also never had the small speakers behind the seats, so I picked up a set of those. This is my current setup and I am really happy with it. I get more power and better clarity out of the whole thing. I think one of the big things is I'm fairly sure the factory amp has all the channel leveling and crossover already built into it. That really helps put the power where it needs to go, even if it's not huge power numbers. It's not nearly as customizable of a setup, but to me at least it sounds way better than anything I've had in the car before it and it all fits in factory locations and uses factory wiring. One thing that is interesting with the sub though is that the factory wiring diagram and the actual car do not agree. The diagram shows a two channel sub (like a dual voice coil maybe), but the wiring does not support that. There are two channels coming out of the factory amp to the sub connector, but the connector on the sub side only has one channel of wiring in it. I don't know if Dodge intended to have two speakers back there at one point and changed their mind late in the game or what, but I have two different connectors from two different sub boxes and both are the same setup. Just something to keep in mind if you intend to keep the factory amp. I am also planning to get a GROM aux input kit for the factory head unit at some point. This more or less gives you modern BT and aux input kind of functionality through the CD changer interface on the radio.
So all this said, I'm not sure what you're going for, so take everything with a grain of salt. I like to think of myself as someone who enjoys high quality audio, but I'm also not the type to spend thousands on a concert level system. I want good value for the money and I value quality over raw power. I also realize the Viper is just not an audio platform and has limited space to do anything. My cam and exhaust also make any audio work far less impactful. Sitting in the car in the garage it sounds great and has plenty of power, but the second I start the engine all the bass gets drowned out. I now at least have the clarity to hear songs on the highway and actually pick up the lyrics, but it's not like the Jag XKR I had where you're riding in a bubble and can really enjoy the good radio it had.