To Answer all of you questions in order
1. Nitrates, water changes are good. The amount varies that some will recommend. I have had Fish Only With Live Rock tanks and used tap water with a conditioner with not Issue for five years. I do use RO/DI water now since I have a mixed reef and I have seen better results. Use a good salt, do not go cheap. Mixing usually is .5 cup of salt per gallon of water
2. Green Algae will take care of itself over time with proper tank maintenance and water quality
3. Most test for Magnesium, Calcium, Alkalinity, PH, No3, Po4, and salinity. There are good kits out there or you can purchase individual kits. Saliferts and Red Sea seem to be the best. I am presently switching over to all red sea since I use Red Sea salt (coral pro)
4. Per reading through this thread and you have Gotton rid of the canister filter, I run a hang on the back for my 72g system and have run HOB for years with out issue. Live rock is you friend for filtration. The more rock you have the more natural filtration. If you increase your volume of live rock make sure you add cured rock. even if you add cured rock you might see a mini cycle from the rock.
5. Right now do not over feed. Make sure you know what you fish eats too. Reading you now only have a clown left? I feed frozen blend of mysis, brine shrimp, and more (made my own) and also some flaked food. I have a tang and I also feed nori (seaweed) the clown seem to pick at the nori too. Nori is what sushi is wrapped in and you can find it at the grocery for pretty cheap. you will need a clip. if you go mix reef then some will tell you to over feed, be careful of how much you feed or yes you will be back to were you are now with high nitrates and phosphates. I have been battling this issue for a couple of month now. I am running a GFO(Rowa)with a small amount of carbon and dose no3-po4-x each tank is different.
6. That seem to be answered. Some like a thick bed for better natural filtration and some like no bed or thin bed. I went with a thin bed of sand.
7. I have not heard to many complainants about the clean up crew or problems. They will die off and you will replace some, but they are beneficial.
8. Get rid of the canopy especially if you are going mixed reef. Natural gassed get trapped under a canopy and are not good for your tank. Also your light will penetrate down to your rock and you will see better growth in the future. You will also have to make adjustment to you light because you to much light you will see the green algae come back. If you are concerned about not having something on you tank get a simple window screen and put it on top you your tank. Also if you decided to not use a canopy I would look into a auto top off unit. I used to keep a canopy on my tanks when a had FOWLER tank and I had very little tops. Now that I do not have a canopy I found that I was ruining everyday to top of the tank and my salinity was up and down for that reason and it was a daily chore. Now that I have an ATO life is so much easier.
Time is your friend. I have been told many times to make small change and wait to see what happens.
Everyone in here has good answers, I just wanted to answer all your questions in one post. Good luck with the rebuild.