Great to hear you guys are busy!
We limit individual jobs to 1400 images. For your situation we would recommend breaking it up into 3 jobs. These 3 jobs can then be assembled by creating a Location Map: http://support.dronesmadeeasy.com/hc/en-us/articles/207455313-Creating-a-Location-Map
When breaking it up into the individual jobs it would be good to include the last pass of one segment as the first pass in the next segment to ensure that that there is plenty of overlap between the adjacent segments.
For example Job 1 would get passes 1-20, Job 2 passes 20-40 and Job 3 would get passes 40-60. The passes 20 and 40 would get uploaded twice to make it so there are no gaps in the Location Map.
We have had people put together triple digit segments to cover 10s of miles of river and roadway using this method.
The Location Map will not combine the GeoTiff images, that will be up to you.