It's been a long time since my post, but I thought I'd put some closure on this. I pulled out the HVAC system and blower over this past weekend. No obvious problem, but I replaced the orange wire and sure enough it works fine now. I recommend that anyone installing the lotus kit also replace the orange wire from the blower entirely. It's only a couple bucks and it could save you a lot of headaches down the line. On the plus side, having done it before it only took a few hours to pull out the system, replace the wire and install. Clam goes back on tonight!
Thanks for the warning, need to tackle this soon and definitely making note to replace this wire!