OK,
Here is what I would do.........
Put the live rock in the 90 that is cycling, assuming you already have some rock in there.
Will you have enough bio- filtration in the 30 without it?
You should if you have some sand or crushed coral on the bottom already. If not, get a sponge filter and run for a few days in the 30 before doing the next steps.
Then, lower the specific gravity ( test using a glass hydrometer........not a swing arm type ) to 1.009 or a salinity of 14 ppt ( if you are using a
refractometer )
When you do this salinity drop, you can do it over a few hours to a couple days. Just make sure and add some buffer to the water and check the pH often as it will drop quickly in low salinity.
Then maintain the low salinity for 3 weeks. You will need to check salinity ( or sg. ) twice a day for the first few days until you get a good feel for the stabilization point.
The low salinity will eliminate cryptocaryon from the fish completely. There is some evidence it can eliminate some types of gill flukes as well, but not always.
Then once you have the 30 tank stabilized for a couple weeks, start the treatment for flukes as follows:
Prepare a bucket with some of the water from the 30 gallon tank ( maybe 3 gallons ), add 0.5ml per gallon ( so 1.5ml for a 3 gallon bucket ) to the bucket and add an airstone for gas exchange while giving ALL of the fish the bath. The bath should last for about 45 minutes. Repeat the bath every 3 days for about 3 treatments.
By this time the fish will have been in this low salinity system for over 3 weeks.
You can then raise the salinity back to normal over the period of 4-5 days, and then they are ready to go into your newly cycled 90 gallon reef.
The fish will not have Ich, oodinium, or gill flukes, and you will be off to a great start.
Just make sure to monitor ammonia levels in the QT, as well as pH and salinity.
Nitrites in the QT are actually not very important ( believe it or not )
I know this sounds like a lot of work, but you will not have to tear down the tank or lose fish to ich either.
Then every new fish you get in should be QT'd in the same way ( except skip the formalin baths if the fish show no symptoms like scratching )
Any questions I will be glad to help..............I have been where you are ( and much worse )
John