Xtech, Black epoxy primer like PPG DP 90 is an excellent product. If you are stripping your panels to bare metal I highly recommend using a light coat of etching primer. The etching primer is fairly inexpensive and you will only need to apply 1 to 2 thin coats( you will be able to see through the primer as it is nearly translucent). Most etching primers have a 1 to 1 mixing ratio so you can mix small amounts to prevent waste. After it is dry just lightly scuff it with a red scotch bright, tach it off and apply your epoxy primer.
As far as painting your panels individually, you will definitely get a cleaner job ( no paint lines or overspray). Just be aware that spraying panels at different times can produce different shading, especially with metallics. If you can, it is best to set everything up and spray all the panels at once if possible. Best of luck with your project!