First and foremost, welcome back! Like yourself, I'm also a Ninja enthusiast and look forward to improve my own performance day by day. So here goes my personal input in the points you mentioned:

1 - Doton is a DPS gain as long the number of targets are 3 or more and they get the full damage timer from it, if not, then Raiton is the better alternative (or Suiton > TA if it's a troublesome target and the boss is nowhere close). The best AOE rotation imo would be:

Katon > (Kassatsu) > Doton > Death Blossom > (Blood for Blood) > DB > (Internal Releases) > DB... then weave OGCD's in between DB's and don't forget to refresh Huton with Armor Crush.

2 - I don't think it's worth it to wait if your Huton timer is below 10s and "Duality" is up or nearly up. It's a very negligible potency loss and Duality is usually synced with "Dream within a Dream" and "Mug" in terms of cooldown and usage so it's nice to have them all lined up for the next burst combo.

3 - As the melee DPS with arguably the poorest AOE capabilities out of the 3 melees, we should focus on what we do best, and that is single target burst but like I said in the previous point, use the AOE rotation if the encounter asks for that, it will always be better than single target damage and will speed up the encounter from your part.

4. Use your utility as best as you can, Ninja has a lot of interesting and powerful tools like Shadewalker and Smoke Screen, although they are more situational and cattered towards end game challenges, it's always good to use them in more casual content like roulettes to create the habit of using them and that will strike you as a proficient Ninja in the eyes of your groupies.

Slashing debuff appliance is our job if a WAR is (very rarely) missing, you'll buff your own damage aswell as the Tank(s), so that's another important 'utility' in our set.