1 mm gravel should be fine.
Please don't set up an NPT until you have a nice selection of healthy plants-- in hand.
Use tapwater, not R.O. water. R.O. water has no nutrients. The lack of calcium in R.O. water is particularly dangerous for plants (my book, p. 114). I'm not surprised that your plants fared so poorly.
You've done a fairly good analysis of what went wrong. Hats off to your perseverance!
