Timeline misunderstanding in Fairy Tail
for how Zeref got to tenrou island
Zeref is immortal and rules over an empire. we can presume that he used one of his ships to get there.
As for when Zeref got there there isn't anything stating the time he got there but I think we can presume that it's like a little get away for his curse of immortality due to there not being too much life around there.
as for how he stopped the invasion he said that he told the shields to stop due to the invasion being something that the shields did on their own. there is also the part of him being a legandary mage so we can presume that he can use some sort of communication with the shields even though nothing shows telepathy or something like that to be his main magic we can presume that he used it just how mavis used a form of communication to tell the other fairy tail members not to go near the guild.
all that I said is with what had happened in the third/final season of fairy tail.