both coil wires fire at the same time, it's called a wasted spark system. So, it's never cylinder specific.
First, disable the TORS, it controls your ignition gound.
Then, easiest test is to check the ground by placing a jumper wire from the engine to the frame. You can use car battery jumpers and clamping one end of one to the engine and the other end to the frame.
After that, it's all trouble shooting.
Most times it is the primary coil. Ohm meaters lie, have it tested on a load tester. These machines cost $300 and take less 2 minutes to verify if your $40 coil is good or not. Most shops will charge you 1/4 there labor rate if the coil is good or it is bad and you do not buy a replacement from them. That's fair since you didn't buy a $300 tester. If there not using a load tester, then don't bother as you can buy an ohm tester at radioshack for $9 and do it yourself.
The CDI is a hope and pray. Even the service manual says check all other componets and replace if no other problem found. At that point it is worth a one hour diagnostic fee to have them say what is wrong.