...your welcome, hope my ideas work out for you
Your list would be great. Let me go one item at a time...
1) I just got the Shapton Glass stone myself in the last few weeks, it is a really nice stone, you would be very hard pressed to get a better stone. You might also consider the Shapton Pro 1500, I do not have it but I have been reading good things about it recently and as you will see below it might help lean up your initial purchase. http://www.chefknivestogo.com/shaptonpro1.html
2) Green Brick is very soft by comparison, I don't think they are exact replacements for one another, though they fall in the same grit range. I definitely prefer the Nubatama over the Green Brick. What you might consider (someone chime in if I am wrong) the Suhiro Rika is said to cut well for a 5k, coming off a 1500 Shapton Pro should not be to big a jump. You could delete the 2k stone in the short term and add it later based on what you learn what your preferences are.
3) I do not have the Suhiro Rika, but from what I have read that should be an great stone to work with. I do have the Arashiyama and like it very well but would not go to war on its behalf over the Rika. If you delete the 2k stone the 5k should be an easier jump.
4) I do not use a stone holder. People like them for giving knuckle clearance and providing for non-slip on your counters, but I just use some shelf liner on the side of my sink so the mess is easy to clean up and my dominant hand is over the sink basin so no knuckle problems. If you think it would be helpful, go for it, but it is not necessary.
5) Loupes are nice...and I have good eyes.
6) I have never used an angle cube. I think this is a "how do YOU learn" sort of a question. The "sharpie trick" is a great skill to duplicate an existing bevel angle so you don't need a cube here. If you are establishing a new bevel you do not need to feel constrained by a specific angle so the cube is not necessary here. Ultimately, which angle is less important that holding a consistent angle. So get the cube if you NEED to know what angle you are working at, but know YOU still have to hold it steady and the angle will work itself out.
7) I use a DMT plate for flattening, if you have the means, spring for the Atoma, most reviewers believe it to be worth it.
8) Lastly, this: "As an aside, I have also discovered the forum specials. Note to the administrator about qualifying--can I access these deals if I have 10 posts and 90 purchases???"