I'm thinking that the +2 from the "Modifier" was not removed(...)
the +2 is still there when I toggle between the "Attacks"
What "Modifier" are you referring to? All things are called modifier

Do you mean the manually added modifier, the ability score modifier, the magical weapon modifier, or the "Modifiers" button...
Toggling between manual and automated attacks only turns field visibility on and off, it will change nothing about the way the to hit is calculated.
I added the +2 (Modifier) to hit for both Sling and Shortbow for the "Archery" in 6.44, then removed it in 6.91, but the "To Hit" was off by 2 (6.91), (selected the Fighter "Archery" and it added the +2 for Range Weapons)
You added them in the 'Bluetext' field I presume? Importing from another version does all kinds of wacky stuff with the sheet. So unless I have your sheet I can't find out what happened. However, the easiest solution is not to import the sheet at all, but just to copy-paste stuff (you won't need to copy much, most things are automatically filled now

).
"Weapon type off-hand" or "Weapon secondary" takes away the damage modifier(...)
That's what it says in the mouseover text, but I'm not sure why you are posting this here.
Does the " Mod" change when the Bluetext changes?(...)
Again what "Modifier" are you referring to? If you do a mouseover of the 'bluetext' field you'll see that it can be used with both a static number addition or a dynamic addition of an Ability Modifier of your choice. The " Mod" in the code that you are referring to is this Ability Modifier.
When I recreate your character in v6.44, export it, and import it in v6.91 everything works fine. All I have to do to get it to +10 instead of +12 is to remove the "2" from the 'bluetext' field. (maybe you have to press the "Modifiers" button a couple of times to see the 'bluetext' fields)