Mitch you're absolutely right that the biggest challenge is making the extra footage stand out as little as possible. The main factor that will make this difficult is that the extended cut of STM was made from a 16mm source. I'm assuming you'll need a 4:3 VHS copy of the theatrical cut to fill in footage lost through commercial breaks and station ID's, such footage will be quite noticeable as it will be from a 35mm source.

GOOD LUCK, I wish you well with this, a lot of Superman fans have been chasing this for some time.