I'd check the pick up first, just because it's easy to do and requires no major disassembly (unless it tests bad, then you have to pull the side cover).
What kind of condition are the High-Voltage leads on the ignition coils? I've heard of a few people pulling the caps and trimming the leads a bit before reinstalling the caps do to cracks and such in the wires. That could cause an intermittent spark problem, but I'm not sure if you'd get the consistant problem you are reporting.
The CDI work is a major undertaking, seperating the casing frightens me a little since if you screw it up you can make the problem worse. I'd tackle that only after checking the rest of the electrical system for faults. Don't forget to check your kill switch contacts as well, mine were dirty and causing wierd missfire/no-start problems for a while.