I think I can explain 2 & 3.
2) A stone was destroyed in 2 instances in our timeline. 1st was when Wanda destroyed it. I think Thanos quickly used the timestone to turn back the clock, before any damage could be done. 2nd was when he snapped to destroy them all. In this case, given how messed up he looked, I think he probably willed it so that his ideal reality remained intact while destroying the stones, which is an insane task. So the stones probably reverted back into their original state in non-stone form, or something similar, to keep reality in-tact.
3) Thanos is a scientist after all and one of the most brilliant minds in the universe. Perhaps he replicated the pym particles and used them to transport his entire fleet.