429 CJ cars had what Ford called the IMCO system, for IMproved COmbustion. It consisted of modifications to ignition timing and fuel mixture. Things that accomplished this included the Q-jet carburetor, the dual diaphragm distributor, and a throttle solenoid which helped to prevent over run on shut off. Another device (often missing today) is a thermostatic switch atop the vacuum distributor fitting (on the thermostat housing) which served to advance the timing (thus boosting engine speed) when the engine heated up during prolonged idle. CJ cars did not use the Thermactor (air injection) system.
429 SCJ cars are more interesting. All of the original ones I have seen were equipped with the Thermactor system, similar to the that on 428 CJ and Boss 429. The biggest difference is the air injection is routed to the back of the cylinder heads on the 429, as opposed to the individual exhaust port areas on the FE engines. I have been told the less precise fuel mixture control of the Holley mandated the air injection to keep emissions under control (It is also said Ford's desire to get away from Thermactor is why they went with the Q-Jet on the CJ. They had to go with the Q-Jet because their own big smog carburetor, the 4300D, wasn't ready when the 429 CJ went into production. The 4300D finally appeared on the 429, but not until 1972 as the 429 Police Interceptor. Both it and the 4300D Boss 351 of 1971 and 351 CJ and HO of 1972 avoided air pumps.)