Lisanna never came to the guild after she got back from Edolas. She hid when she first arrives and reveals herself to her siblings.
She does get stuck in the 7 year sleep on Tenrou because she went there with Laxus to help her siblings. Laxus and the thunder legion know about her return because of how close to the Strauss siblings they are.
Instead of Lisanna being Juvias team mate in the S class promotion exams its Lily. Carla was allowed to tag along to the island since she would have been the only exceed left at the guild Makarov allowed her to come as long as she didn't interfere.
The E.N.D book is destroyed, but the power and changes it caused in Natsu are still there. Similar to how the dragon seed changed him the demon seed did so as well.
Spoiler for later chapters!
Lucy rewriting the book also caused changes in her, but I'm not going to give her an huge power boost, she's going to be a bit more powerful than she is in the 100 year quest Manga. Natsu will technically have a power boost but honestly not by much, he is just not going to act as weak.
If he can defeat Jellal when Erza couldn't in the tower of heaven ark he's stronger. Sure maybe she emotionally couldn't, but what about all the other top baddies he defeated. He defeated Zeref and right after with his injuries took on Acnalogia. So really I think he's stronger and technically it's also said by Erza in the anime, that he adjust his power and fighting based on his apponant.