I have two grates in mine. The top grate is 5 inches from the top and the bottom grate rests on the lip where the tamale steamer goes. I drilled holes in the bottom of mine so I place an aluminum pan on a trivet on the bottom that I use as a deflector and/or drip pan. With this set up it gives me 4.5 inches between the grates.
The picture below is with the bottom grate in place. The bolts and nuts you see are mounted from the inside out as I found that the best way to place them to holding the top grate. When I placed the bolt heads on the outside it made it more difficult to emplace and remove the lower grate.
Good luck with your mini WSM project. I love mine. There is a bunch of info posted on these over on the Virtual Bullet site in case you have not already checked it out.
WSM, 99 & 09 Performers, 2-OTG, SJG mini WSM, Summit 420, Q100, Akorn, and Schwenkgrill