Two step only working in neutral!! HELP

The 2 step on my msd sb6 only works in neutral now. With the msd program opened up on my laptop, I can pull the clutch in and it’ll show clutch in (being in neutral). With the clutch still in I’ll put it in gear and the laptop will show the clutch is out even though I’m still holding it in. I’ve been back and forth over everything. It was working before. I had to tear the bike down since I cracked the frame. First gens had a weak spot. Was working before. All my connections are correct. All wires ohm out correctly and do not ohm to the frame(as if a wire was pinched). I replaced the gear position sensor because the readings weren’t perfect. There’s even a relay box in the tail of the 14’s that the neutral wire runs to that I replaced. For some reason the two step is loosing ground when it’s put in gear. I can make the bike think it’s in neutral but actually it’s in gear and the two step works but neutral light stays on. Got me stumped. Hopefully one of y’all have some suggestions!