How would it effect the handling if I was to go from a 40mm offset to a 43 or a 45? This would be on a 56cm Trek 5900. I noticed that the one size smaller 54cm came with a 45mm offset. I am going to get a new fork but I cant seem to find one in 40mm.

It would give a slightly softer ride and make your bike a little more stable at speed. Your handling would get a little less twitchy.