Ok. It's ridiculous I know. Very hard but here's how I finally got the diamonds and maybe you already know this trick but I'll tell you anyway. And I'm sure those of you who already do this are cursing me! Sorry about that but I'm trying to help those who are near tearing their hair out!
The best place is to start at the Basilica where Drake is. There are several spawn spots there but you'll only ever see one ore at a time. Then go into the athenium and while you're at it look for the lava lilys to the left or the right. Then procede up to the minigame area. There are four different spawn spots for ore. Two spots are in front of the two minigames areas. The other two spawn spots are behind you to the right of the Tower Archive doors. There are only two ore spots at any given time in this area. One could be in front of a minigame and the other to the right of the Archive doors. Or two at the minigames or two to the right of the Archive doors. Past that in the area behind the one shop are two spawn spots for stone blocks. Stone blocks give fossils from time to time. BTW lava lilys occasionaly give fire blossoms. Anyway now you've done the first run. Next, switch realms and do the run backwards to the Basilica. Each run takes about a minute (if you stop for lava lilys, ore and stone blocks), which is how long the delay is before you can switch realms again. Switch realms and repeat till you've done all the realms. Once you've done all the realms and if you're not too bored out of your skull you can repeat starting with the first realm you began with. By this time everything has had enough time to respawn. BTW I would start with Wu, the last realm, and go backwards. Other people do this run and most probably start with Ambrose and work their way down to Wu. Plus, the game usually loads players just signing on to the top of the alphabetical list and then right on down the line. Population of Wu is almost always "perfect".
Best time to do this is very early in the morning or very late at night. I had the liberty of doing the runs at 2 am from time to time. I could get around 5 to 7 diamonds in one pass through of all the realms depending on how many people were playing the game.
Commmonly known as the diamond run it's best done by yourself and not with friends for obvious reasons. Put on a good movie while you're doing it cause the switching of realms, although more productive, is boring as all get out. Hope this helps.
And further, wait till the next crafting quest where you'll need a slew of black pearls! Back to Mooshu for that and switching realms. Ugh. I haven't even started on that yet. lol