Problems like this can be very frustrating, even for experienced mechanics. A couple of pieces of advice/things to remember:
1. If the cylinder has sufficient compression, approx the correct fuel/air ratio and a spark at approx the right time, by the laws of physics, it HAS to run. Keep this in mind when you get frustrated.
2. Start with the simple things first. When I worked at the shop we had a rule that we ALWAYS put fuel in the tank before we started to work on the bike. In this case, I would start with:
a) Put a new plug in. (or swap one from another cylinder.)
b) Check the plug cap. I've seen lots of cracked plug caps causing problems.
c) Check fuel lines, etc. Best to check fuel by pulling the drain from the float bowl, make sure lots of fuel comes out.
d) Check the coil wire to the cap for damage. Look for cracks, melted patches, etc.
e) Swap the leads out with the alternate cylinder on the same coil. As previously mentioned, the coil should fire two cylinders at top dead centre.
Let us know how your making out. I hope this helps.