Matt my 250 has done same thing for around 10 months. Ive chased everything like you have.  New primary coil new pick up. Different cdi different  coil. Checked all connections. Checked harness. But mine doesnt run right first threw 3rd. I have 400 main in. But I can pull a 450 clean threw 4 th threw 6th. But will not pull it till 4th.. but mine has flashes were it runs right for a pull or to then back to crap. Im pulling motor apart this weekend im going threw everything. If I figure mine out il let you know asap.