If the Orange wire at the blower isn't completely replaced by the kit, it is probably badly oxidized under the insulation. Does the kit include a new orange wire? The black wire is probably OK.
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!