You are right in keeping the MSD box in the open and make certain it is grounded well. I don't recommend enclosing it all. A guy in our Chevelle club had one mounted on the plastic inner wheel house of a '72 Chevelle and didn't have a dedicated ground wire and it overheated and started the plastic on fire. There wasn't much left of the front third of the car by the time the fire department got there and put it out.
What you have done to make that Nova better than new and more fun to drive is amazing. Enjoy it... 
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Mitch
1970 Chevelle SS
1966 Chevelle SS
1967 Camaro ss/rs
1938 Business coupe, street rod
2000 FXSTS, original owner, 13k miles
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