2003 MDX - 2 issues: Transmission & rear A/C

Just replaced the transmission with a rebuilt from Japan, works great but now the D5 indicator begins to flash after driving for several miles. Independent shop put analyzer on and message seems to indicate that the onboard computer is not reconizing the transmission. Does anyone know how to resolve this? Also, after the transmission was changed, the rear A/C does not blow air. The dash REAR A/C light is lit and so is the light on the rear console display. The fan fails to move any air regardless of setting. These two issues could be totally unrelated but it cause me to ask the question anyway. Any help would be greatly appreciated.