1000 watts of HID for one plant seems like a waste of light to me. I would use the smaller light for just the one plant. I would also start flowering ASAP. Some plants such as the sativa dominant strains could triple in height by the time theyre finished.

1 1/2' from the tops of the plants is about right. The closer you can get the light without burning the tops of the plants the better because light intensity diminishes quickly the farther away from the source you get. 18" from a 1000 watt light is perfect IMO.

As far as your germination success rate, I still stand by the old tried and true method of planting the seeds directly into the large pot that they will live out their lives in. A large pot of soil with no roots in it stays moist for a long time and helps germinate the seeds. Plus you don't have to handle popped seeds and possibly damage the young roots.

Hope this helps.

Laterz