With ref to the strings not aligning, this is very common on Fenders. More often than not it's a fairly simple but slightly scary job to put it right. I've done it a couple of times now.
You need to loosen the neck screws and then exert some force on the neck (you need firm pressure but don't be heavy handed), from the head stock end, in your case pressure on the top and push down. This is sometimes easier with another set of hands. One person to push and the other to then retighten the screws.
Another option would be threaded saddles as used on some of the vintage Fenders, which allows you more adjustment.