Yes, everything you listed is the correct steps and order to perform them in. Well, the JB4 is just a piggy back so that can be taken off whenever unless the MHD tune is setup up with something specific for the JB4.
1) Remove JB4
2) Use MHD to Flash back to Stock Map (noob move of course...)
3) ...
4) Profit (Sell the car to someone who will tune it again
