Toby's age nor him himself doesn't bother me. Keep him in the movies. As for movie years, I would have a year or a couple of months difference.
I would have it where Peter and MJ are repairing and patching up their broken relationship. Peter feels that there's still a chance he might get a second chance on handing her an engagement ring once again and pop the question to her but only time and fate can decide it all. Peter is working as an assistant for Doc Connors and still shoots photos for the Bugle.
New York is safe---for now but when Peter encounters two thieves named Alex O'Hern and Herman Schulz (aka Shocker and Rhino) and disposes of them early in the movie. He feels that his crimefighting work is far from over. We later learn it really is, as Connors becomes The Lizard and Kraven the Hunter comes along to make matters even worse.