I am restoring a 1984 Honda CBR 400 F2. There are two coils and two CDI units. There are 4 wires coming from the firing pick ups; yellow, Blue, White/'Blue stripe; white/'yellow stripe. Each CDI unit has 4 connectors in a six pin mini connector, the middle row is empty.

Can anyone help me determine what wires go where?"

 

A quick Google pulls up a wiring diagram on this site:
http://www.fireblades.org/forums/honda-cbr400rr/78704-wiring-diagram-for-cbr400-er.html

It'a about the 8th post down. I can't look at the detail, you need to join the site to see it.