Hi and welcome Nick.

I have not done this kit, but the tongue part of the neck also looks wrong to me. Also, it does not represent the picture of the kit on the PB web page. I also cannot find a similar build diary - but I'm sure I have seen one!

Don't cut it back! I would use the scale length for the high e string area to see where the neck must be positioned to achieve the 628 mm scale length. This should at least let you know if it is the step that needs to be removed.