Thanks for reaching out. Impressive project. Hope it turns out well! So with the number of GCPs, I would recommend 5, but you can place up to 10 GCPs in a given map. More information on that can be found here This article will give best practices when using GCPs.
A good number for Side/Frontal overlap would be about 75/75. I would bump this up to 80/80 personally. However, this may increase the flight time thus increasing the number of batteries you would need to complete the flight.
You may use two drones to map the same area. You would just need to make sure that your photos are geotagged and the file numbers are not the same to avoid the risk of overwriting your data. I would set the altitude the same for both flights. The accuracy will be better if you flew with one drone but I believe the variance will not cause drastic errors.
Thanks and let me know if you have further questions on this project. @consultant