Okay, I've found and squashed some bugs in your sorting system! ;P
First, there is no glowstone dust or lapis in either the machine room, or the back of the sorting machine
2nd, there is no need to have sapphire ore, emerald ore and ruby ore, since they just drop the gems, and they're allready categorized
My solution was to simply replace the gem-ores with glowstone, and lapis, its a makeshift bugfix, rather that, than my 3 stacks of glowstonedust getting trapped in the infamous "Overflow chest"
Also, regarding the oilwell, its probrably one of the biggest you can find - not that I have explored the rest of the map yet, but the bigger the fountain the bigger the resevoir I believe, and that ravine the well goes through, might be considered surface, and from the bottom of the ravine to the actual surface - thats a big ass fountain.