A little advise: do not make sentenсes longer than half of the line. You pick different ideas and merge them into one sentence, making it very hard to understand what are you trying to say. The last sentence of mine was about half of the line, and it is pretty long, but it is 2 times shorter than yours.
Not all, but one quest. 1000cycles is freaking 42 BILLION EMC, being 5250 (2 double chests) of red matter. Damn, for this cost I would never run a reactor, aspecially if there is 0.9Billion EMC Solar generator producing even more.
As a server admin, I have experienced a lot of problems with these computers. So, the best solution I and my crew came up with is to replace ComputerCraft with OpenComputers, where you can do anything LUA allows you to, and, despite from those computers being very far from "easy to use", they provide almost infinite possibilities, for players and map makers. I have not yet had a look on your Command Block system, but I will definately do that, because there are pretty nice Thermal Expansion teleporting pads, allowing for user to get anywhere in a certain range.
I have read all the 32 pages and also all issues on GitHub.
And Happy Birthday! Enjoy your vacation!