I like the idea that you are going with the black on the engine instead of the orange. I painted my engine black and have got a bunch of comments about it. I'm not sure what you can do to make sure the paint sticks to the motor. Besides scuffing the paint a little bit then cleaning and then spraying it black... that's all I would know to do.
Make sure when you install the frame connectors that the car has the motor installed, seats, basically complete then have them welded in WITH THE CAR SITTING ON ITS OWN TIRES. Then have them welded in.