I got my level 30 clone and went and did some experimentation. Uptil now I've made sure not to turn in any ToO quests. The toon I did the original leveling on has Wilderness ToO complete but did not turn it in. On the clone I got the ToO quest for wilderness again. Immediately it did complete for waypoints, logos, operations, assault cps, and defend cps. It did not give me complete for Thrax, Miasmas, Xanx, Shield Drones, Officers, caves, and story missions. I went and did all the kill ones and the caves so all I had left was the story missions. I did /petition that I couldn't complete it. In the mean time I went to Palisades, The toon I leveled on has not done the cp quests and not done all the ToO kill targets for Palisades. I immediately got compelete for logos and Ops. I went and talked to the eloh vale transport guy again to resummon the dropship. This gave me storys complete in Palisades. I was then able to do all the kill X quests and the CP quests and get a Palisades ToO complete. Along the way a gm contacted me. He asked me if the character having trouble was a clone. I told him yes and he fixed it for me so I got story complete and hence Wilderness ToO complete.

Conclusions:
1) Turn in CP quests right away, don't wait to clone. Since you could transfer tokens between characters I thought I might just turn them in on the clone so it would get credit but it seems the clones get credit too for ToO purposes.
2) You can complete ToO quests on clones that did not do the story missions. It may be bugged and not automatically give you credit but you can petition and get credit
3) (I haven't seen this first hand yet, probably won't see it first hand before i hit 50) Don't turn in ToO quests before hitting 30 and even then turn in 1 and don't turn in another until you use the clone credit. Clones can't redo quests so I'm guessing they can't redo ToO quests. If you turn in a ToO quest before cloning, then the clone probably won't be able to do that quest. So if you wait, the clone and the original can both do the ToO quest and both get a clone credit.