This may seem complicated but once you have your lists done its well worth it, the ease at which you can farm is something else.
First off when sending out these runs always set your hero gear to Intel as it seemed to increase the drop rate.
You want about 5,000 ballista and 5,000 transporters per city.
You want to set a troop preset in your rally spot of 550 ballista and 500 transporters.
Write down the co ordinates of the 8 closest lv5 NPC's for each city.
Next, write down the co ords of the 8 closest lv4 NPC's to your cities.
Go into your rally spot and select a level 100 hero in your city with full mount gear (level 10).
Enter in all the co ords and write down the times beside each NPC.
Next you need to get the list of 8 lv5s, and 8 lv4s for each city down to just 8 NPC's.
You want as many Lv 5 NPC's for each city to hit as you can, so write down now any Lv 5 NPC that is 30 minutes or under. If you cant get 8 Lv5s for each city you need to substitute them with Lv 4s.
So lets say you get five lv5 NPC's within 30 min, pick the three closest levels 4s now, should also be under 30 minutes.
Now you should have a list of 80 NPC's to hit (8 for each city, when you have 10 cities). The list should contain mostly Lv 5 NPC's with a few Lv 4.
Next you need to organise the co ordinates, Find the fastest run for each city, this is the run your attack hero will do. The reason being you want your attack hero sent first to the closest NPC so he arrives back quickest because you need him to defend your city.. This will mean you will have every available hero out at once with only mayors remaining. You should be able to find a LV4 or 5 NPC within a couple of minutes from your city.
Finally you make your final list. Place the fastest run for each city, its co ords at the top of the list. Now with the other 7 co ords for each city arrange them according to number value, e.g. 620 first then 621 etc. After you order all your co ords you will notice many are nearly the same. So all you will have to do is change 1 or 2 numbers in each co ord and then send. It means you can input the whole list into the rally spot in probably under 1 minute. Because all your runs are under 30 minutes to and from the NPC's it means it will only take an hour for all your runs to return.
But this only applies to LV 100 heroes because we judged the time by him leading the attacks. So if you don't have all lv100s your attacks will take longer at first until they are full. But once they are, and they will be very fast, you have the most efficient gem farming system at your disposal there is.
Now its up to you how often you send. If you spend hours upon hours on the game you can acquire vast amounts of gems in little time. You want to launch every hour and if you spend about 10 hours online, you want to be sending 10 runs. You can average 50 gems a run, sometimes more, sometimes less, when your colony quest is full and you have all LV100 heroes. That's about 300 a day from 6 runs or 500 a day from 10 runs. Its possible to acquire thousands in weeks and make a very high start set.
You will notice a ratio of about 4 orange to 1 blue.
This is a guide to what I have found to be the most efficient system. Of course you can always add high level NPC's to each city as shown below using the same system. Here its done on Microsoft excel, but you can write it out either, its just as good...