1> This one can be accomplished in the new class you're creating in the editor. there are to buttons that allow you to modify the spells available and the how they progress by level. see below.
2> ITs difficult to help on this without knowing what was added and where. It could be a timing issue (as is often the case) or the code you "cannibalized" is looking for old reference points as it relates to the scout. Sendric, Fox of Shadow are better at defining the exact code smith wording, but without seeing what you are doing its difficult to help. I would suggest a sampling of your code or a link to the User file so its clear what is being done and the goal to accomplish.
3>
Not sure what you are referencing... is this Smite of Sacred Fire from the "Forge of War"
http://dndtools.pw/spells/forge-war-...ed-fire--3558/
Hope it helps