Signed in under wrong name

I used the gospel library app for 2 years under my wife's account not knowing it wasn't mine. I recently was put in the bishopric and need to download manual 1 and couldn't which is when I learned i was signed in under my wife's account. She doesn't use gospel library and all of my annotations are in her account. is there a way to transfer all of her annotations into my account?

Yes. Manually.

You could contact the tech support folk for the church. I'm reasonably certain they could do this via query or some internal tool. How long it will take to get that resolved, I don't know. The only way I know to contact them is via the website (which has more options for specifying the type of feedback you're giving) or the feedback link in the app.

With Gospel Library 4 for Android (which should be released next week, or you can get the Beta now) it will be possible to copy all of your annotations from one account to another. Unfortunately, if you have iOS there's no simple way to do this (unless you can borrow someone's Android device temporarily).

Here are the instructions for Gospel Library 4 for Android:
1) Make sure you're signed in to Gospel Library (using your wife's account) and that all of the annotations are synced to the device.
2) Sign out, and choose the option to keep the annotations on your device.
3) Sign in to your own LDS Account, and choose the option to keep the annotations that are on your device.

Note that this will copy your annotations from the one account to the other – they will not be removed from the original account unless you do that manually.