How much of this is against the EULA?

So let's start with your ranks..

You are allowed to sell in-game items so long as they don’t affect gameplay
We don’t mind you selling items in game, but they must be purely cosmetic. Pets, hats, and particle effects are OK, but swords, invincibility potions, and man-eating pigs are not. We want all players to be presented with the same gameplay features, whether they decide to pay or not.

There is one exception to this rule – capes! We have a lot of fun making cool capes for extra-special members of our community and Minecon attendees. We’d like to keep them as exclusive as possible. So, yeah, no capes please, even if you’re giving them away for free.

Also another quote from Mojang at https://account.mojang.com/documents/minecraft_eula

give copies of our Game to anyone else;
make commercial use of anything we‘ve made;
try to make money from anything we‘ve made; or
let other people get access to anything we‘ve made in a way that is unfair or unreasonable.

So they've stated you're not allowed to make commercial use of anything Mojang has made (this would mean items of all kinds), except they have specified that you can only monetize PURELY cosmetic enhancements. Stuff like blocks, diamonds (resources) may not be considered cosmetic because they have practical and functional uses (to be made into armor or blocks for building).

Providing a convenience (your bonus perk commands like /workbench) might not be considered against the EULA because it isn't a 'product' of Mojang. You'd need to make sure that the plugin developer who made the plugin is fine with you monetizing the use of their plugin though.

let other people get access to anything we‘ve made in a way that is unfair or unreasonable.

So let's use /workbench as an example here. I'm assuming it's used to access the crafting table without the need of placing down the block and using it. Providing a convenience for being a donor may not be considered unfair or unreasonable. However, limiting a player to ONLY being able to use a crafting bench if they were a donor would be considered unfair.

Since I went a bit nuts of with this post and it's now a full-scale essay, I'll keep the rest short. You should now understand the EULA better and know what is considered acceptable.

Basically DON'T sell blocks or armor. So long as it has functional and practical use it could be considered to be against the EULA to monetize it.

/fly and /god may be considered to be unacceptable as these are already features in Vanilla Minecraft (creative mode) provided by Mojang turning it into a command and making people pay for it doesn't change it, it only makes it a convenience. I'd consider this against the EULA as you're limiting creative mode features to exclusively people who pay.

I'd also like to note that you have listed access to a donor exclusive area, I'd recommend adding this to all of your donor ranks. Read the following for more information why.

You are allowed to charge players to access your server
So long as the fee is the same for all players, you are allowed to charge for access to your server. You are not allowed to split your playerbase into paying, and non-paying users, nor can you restrict gameplay elements to different tiers of player.

Basically, if you’re charging for access to your server, you are selling a “ticket” and there can only be one type of ticket, regardless of how much people are willing to spend.

So long as the fee is the same for all players, - Yes you're charging a flat fee to everyone for access to a specific area, however..

You are not allowed to split your playerbase into paying, and non-paying users.

This being said, you are charging the player to access a specific area for a set amount of time. A player should donate and have ALL the available conveniences for a fixed cost. Having a ticket to access the donor area and calling it a 'perk' doesn't make it any different from say selling a week-long pass to Disney Land.

As you can see, Mojang is fine with monetizing premium access to the server itself, but maybe just not to specific locations.