I am currently gathering all the equipment to start a build on my 17 denali W/Bose so i cant speak to much about the install side of things from my experience yet but i have talked to a couple who have done a number of these trucks. Did you have a budget in mind to start with?
As far as keeping the stock HU you can use that nav-tv which is nice but like stated expensive, I haven't talked to anyone who has used the llj harness but it looks good to, I will probably end up ordering my amp rack from them and modifying it to fit. They also sell speaker adapters and a couple other things for these trucks. I will be using the pac ap4gm61 to get optical from the head unit but you can also use rca depending on your set-up. It's about half the price of the nav tv and seems to have all the same features.
https://www.crutchfield.com/p_541AP4GM61/PAC-AmpPRO-AP4-GM61-Aftermarket-Amplifier-Interface.html
Pac also makes a harness that plugs straight into the bose amp and if you decide to go with a sep amp you don't have to run any new wire. As long as the new speakers are going in the same locations. https://www.crutchfield.com/p_541APHGM02/PAC-APH-GM02-AmpPro-Speaker-Connection-Harness.html
I got a mti box for my truck with 2 JL 13tw5's - they make a bunch of different options depending on your budget and how much bass you want. They aren't cheap but very well built and can be customized to whatever you want. https://mtiacoustics.com/
If you search around you can find a basic prefab box for around $200 depending on the configuration. Ive also talked to a couple people who have done the jl center console box and they have been really happy with them but like anything else could have some rattles that you might have to chase out. The kicker seems like a good option to..
I will be going active 3 way up front with audio frog gb10 in the a pillars, gb25 in the stock dash location and gb60's in the doors. You don't have to get that crazy, many companies make wide band speakers that could be better replacements for the 2.75 in the dash and then just upgrade the doors. Audiofrog makes a gs series as well that is made to integrate into stock locations easily, focal has a integration series as well that could run off the bose amp and still be a nice upgrade.
I don't think any of this is hard as you think and based on what you have already done to your truck you should be able to handle this but if you feel overwhelmed you could always take it to a local shop. Either way it's not a bad idea to get a quote from a couple places and see/hear some stuff in person anyway.
Here's a couple pictures of my box and pillars. Now i just need winter to get over so i can start already!!