Assuming the bypass was done to the correct wires, the cdi shouldn’t matter since it is bypassed. The only thing I can think of would be the harness. If one of those wires are broken or grounding out, it might cause that and explain why your bypass didn’t work. Hopefully someone more versed on it than me will chime in.
94mm bbk, +4 stroker, Hot Cams, Vertex piston, FMF Power Bomb header and Power Core can, KW black diamond valves/dual springs, FCR39, K&N, Elka long-travel LT fronts and rear, Houser +3, +3/4 LT A-arms, American Star pro xs chromoly tie rods, Dyna non-programable, Tusk +3 axle.