The questions you ask are not answerable by any one person, or one thread. Everyone will have different opinions and if they all posted on yout thread you would have your head spinning.
Your questions about what equipment completly depend on what intentions you have, what your buget is, your location of your set up regarding room constraints etc.
As for LR, Sand, Etc... My opinion is to stuff as much LR in the display as you can, but I also prefer a stuffed display and smaller/less fish
Others would say you should put a deep sand bed in your refugium?along with cheato and live rock. I would stay away from crushed coral unles you are running a bio filter (fluval etc) but most here prefer the bio filtration provided by live rock and sand.
Any live rock is good, just depends on what look you like... but make sure you place it so that as much surface of it is exposed to the water as piossible to maximize filtration.
Make sure whatever you do is take it slow (i am bad with this and have had bad experiance because of it)
Lastly, look on the build threads...search for 90 gallon set ups and see what others have done..
Your Bio says 5 years reef keeping?
Good luck
