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I'll answer what I can. Others will fill in the blanks I'm sure.

We are going to try setting up a saltwater tank again. We were looking at doing this over a year ago but it didn't even get started.

We are looking at a 50g tank that comes with a Fluval u4 filter. We have a fluval fx5 filter unused we can use instead. Tank is currently freshwater so will have to be converted.

We are looking at a clownfish(maybe a pair), a flame angel, bangaii cardinal and a firefish goby as stock if possible and building around that. We anticipate it will be 3 months before we add fish based on research so far. It will be a FOWLR tank with perhaps a lone anemone for the clownfish if that works.

Couple questions before we begin this journey.

1. Do I want to go with the larger fx5 filter (capable of 900gph with no media, we previously used it on a 60g african cichlid tank. It can be adjusted.)?
I'll leave this for the experts. They'll explain it better.

2. Is a sump Mandatory? We have a 35g tank empty right now we could use, but no idea atm how we would connect the two tanks.
I would say yes to the sump. Anything larger than 20-30 gallons should have a sump.

3. We have 30lbs or so of "live rock" It's been dry for over 2 years but still has the remains of the former cleaning crew on it. How would we go about making this usable again? I know we'll have to eventually buy a bit of actual live rock and let the organisms move on over to it but I'm thinking we'll have to cure it or something first?
Scrub that old live rock and you should be able to use it. You could seed the tank with some cured LR to get the total up to 50-70 pds total. Might speed up your cycle process a bit.

4. Protein skimmer and UV sterilizer, are they mandatory?
Protein skimmer yes. UV? Don't know if that is neccesary or not.

5. Do I need high output lights for my planned set up? Can I get by with standard t8 aquarium lights?
You could get by with your t-8 if you didn't go with an anenome but you'll never truly see all the great colors of your fish with that light IMO.

6. With freshwater fish you usually medicate the entire tank when necessary. I'm reading that with saltwater you have to remove the individual sick fish and treat them separately? Does this mean I would have to have 2 tanks going.. with all accessories as well?
Short answer is yes but it all depends on what your medicating them for. Also, you'd have a up and ready QT for new fish.

7. Is there any better or best brand of salt mix? What is the best way to get the salt into the tank?
Instant Ocean has worked great for me.

8. RO water is mandatory isn't it?
Depends on what you tap water is like. 90% or more folks here will say yes to RO/DI water. I'm in the 10% thats been lucky so far and hasn't had any major problems using treated tap water.

9. Refractometer or Hydrometer?
I use a hydrometer. SOme will say refractometer.
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