I was re-reading this topic and had a few thoughts about the writing until you mentioned later the different names Jean/Ann/Anna were registered under. Having done a fair bit of trinscribing for FREEBMD, I would agree with you on the curly bit on an "A" might look like a "J", have had that eye straining problem a few times when transcribing, and I have to agree that that is a possibility. Jacks suggestion sounds like a good way to try and sort this out.
As to the James Fraser (alies (sic)) Fletcher, I would go along with the idea that that is another name that he was known by, for what ever reason he had at the time. On a previous topic if a recall, someone mentioned that it was not illegal to use another name in Scotland, providing it was not for illegal purposes.
Is it possible that "Fletcher" is another family name that James adopted for purposes now only known to James?
This post is probably not much help but it was just some thoughts I was having when reading the posts.