Welcome, Tim.
If I understand the questions, you don't need to get the concrete tub walls flush with the framed walls above, you'll want to get the framed walls above flush with, or a bit proud of, the concrete tub walls below. Much easier proposition.
Raising the drain to the new shower level is just a matter of extending the riser pipe and attaching a new drain appropriate to the shower construction method you've chosen, but not yet shared with us.
You can build up your existing tub floor directly on the existing tile. Again,
if I understand the question correctly.
As for any mold, look in our Liberry and you'll find some information about that. Kill it and move on with the project would be my advice.
A photo or two from a bit further away would likely give us some needed perspective.
My opinion; worth price charged.