You might want to clarify the Koops Rules to avoid any potential confusion in the future. It just means no crits and no cave skip. Other damage boosts from the run are allowed AFAIK.

I've added that you can't take swamp damage either in the run to the rules and how to get past them in order to avoid any possible confusion. I don't think that was going to be a problem, but better to make sure it doesn't based off slightly vague phrasing.

If there is a Reverse Dungeon Order category, perhaps a True Mansion Order run should also be considered on the NES and FDS.

Worst case scenario, Anniversary collection runs could always be submitted as an emulator category since that's essentially what the Anniversary collection is. Glorified emulation on modern consoles.

I decided to make a bunch of save states for beginning, intermediate, and advanced players for the Everdrive and posted it on the resource page. It's more to give newer players who have the Everdrive a set of save states they can download and work with. It covers most of the run with the differing difficulty levels in the run itself.

Thanks to Canight, we have a practice rom for CV2 that shows Simon's Y Subpixel value in real time. Tested it and it works on my Everdrive fine with the subpixel value listed on the top-right corner of the screen. Someone will have to test to make sure it works on Powerpak just to be 100% safe. Have fun experimenting with floor drop setups!

Can you please not badger the mods in the forums every time you get a PB?

To answer your questions:
1) Shikaroxen's (goes by Xenkaroshi on Twitch) tutorial should be sufficient enough to tell you all the floor drop setups (some of the setups are a bit outdated but for learning the run they're all useful). As for save states you'll want a save state for all the double floor drops, blob boost, and the quad drop. On an emulator you get 10 save states.
2) Emulator runs are allowed. Either FCEUX or Bizhawk would be my recommendation. When you submit a run, make sure to check the emulator Box and preferably list the emulator in your run description. Emulator can be a bit of a problem with any% given the number of frame or pixel perfect tricks in the game due to input delay vs. NES on a CRT.
3) I use Livesplit as my timer. It's very easy to find on a Google search and download (it's free). As for frame counting runs (I don't frame count runs unless the 5-8 frames make a difference in a submission time), I use Virtual Dub and count from a downloaded highlight off Twitch. Make sure to install the mp4 codec for Virtual Dub or it can't process mp4 videos (Twitch VODs are mp4).
4) Link: https://discord.gg/pfmjDN

I got it down to 3:10, but the biggest missions that could kill the run are Framed, Lord of the Plains, and Dragon Lair because the route involves putting Kaiba through a gauntlet of battles. I might elect to go with Healing Items to counteract that issue in Framed and Lord of the Plains. I'm going to see if the route can also earn enough money to get the 18 power up items I need to run this full blast. Once I have the best run routed and complete a run, I'll post a guide to this page for anyone interested in running the Kaiba category without the Money Cheat.

I'm currently working on routing the Kaiba story, which IMO should have 2 separate sub categories for money cheat and no money cheat (same with Yugi Story). I currently have it down to about 3:25:00 for anyone that runs to run the category today and possibly could get it down to a 3:20:00.