-So, first thoughts are, your original build pic had the coil way too high, lower it down about 1mm above the air hole. You will have to build a new coil as this will probably just crumple the legs you have on that one.
-If you've already done this, the next question is - how much yarn are you using? Are you just cutting off a length and doubling it over to pull through the coil? My suggestion is, credit to mackman, if your yarn has 4 separate strands, pull one strand out, then double it over to pull thru coil. This will effectively give you 6 strands thru the coil, works perfect for me.
-I don't cut my wick so short that it only brushes the deck, but I also make sure to keep the juice holes clear when I push the wick down into the sides.
-As for the fill screw oring, you're in luck - it doesn't have to be exact, as long as it will fit down in the screw recess and be compressed by the screw head it will do it's job. Maybe fish around in the spares bags from some of your other devices and see what you can find. Home Depot also sells some very small orings in the plumbing section. I think it was a #64 that people have used to fix the insulator on SVD/Vamo center pins and that size should work for you.
-Two things to do when filling - if you're using the blunt nose on the bottle, make sure you jam it in there tight. If you're using the plastic needle tip on a bottle, try screwing it into the hole - it almost fits and helps. Otherwise get yourself some metal needle tips for your bottles -
http://www.mtbakervapor.com/accessories/blunt-needle-tip-for-dropper-bottles/ - or get some sort of syringe to use.
-You "can" fill from the top, but it's a bit tricky and I've always gotten some small amount of leaking from the airhole. The trick to perfect is this - all bottom bits/tubes assembled, only the top cap removed, fill it up to just under the top of the chimney. Put the top cap on, but only screw in a few threads, no more than half way. Now flip the whole thing over and quickly tighten the cap down the rest of the way. What this does is move the juice away from the holes going to the wick so that when the pressure builds from the top cap being tightened, the juice won't be forced into the "chamber" which causes leaking.