I had the exact same issue, I tested everything and it checked out, I replaced my CDi with one from Mike's ATV and never had any problems since ....
1983 Honda ATC250R
1983 Honda ATC200E BIG RED (sold)
1984 Honda ATC200E BIG RED
1984 Honda ATC200X (sold)
1985 Honda ATC70 x 2
1985 Honda ATC250ES BIG RED
1988 Honda ATC250ES BIG RED
1995 Honda Frankentrike 50cc 2-stroke
2001 Honda TRX90
2004 Honda TRX300EX (sold)
2008 Honda TRX250TM
1976 Suzuki RV90M (sold)
1967 Vespa Primavera 125
1958 Massey Ferguson 35