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06 Raptor 350 No Spark, need advice.

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 Ok I've got a 06 350SE. Bought it from a guy starter and ran just fine. Took it to a friend to have it torn down and cleaned. Well he found a hole in the case from chain slap. 

Found a bottom end from a late 90's warrior and swapped it out. He has gone through the whole motor and checked everything mechanically and everything is good. Valves are good, cam, piston, timing, flywheel etc are all good. It's got a brand new stator and ignition coil from rickystator.com. Brand new spark plug. Using the same CDI but bought a new one. All the grounds have been cleaned and are tight. It's got a lot of compression when she turns over it's just not sparking. 
Weird thing is the neutral and reverse lights aren't wanting to come on and we've replaced the harness and bulbs. Saw the reverse light once. Changed the neutral safety switch out and still no neutral light. We didn't really mess with the wiring when we changed the bottom end out. The kill switch was working before the swap and so was the key switch. The only thing that's changed is the bottom end, a new stator, new ignition coil, spark plug and now no spark. Timing is set.
Any ideas on what direction we should go? Thanks in advance.

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