Robby,
the way I would try to do it is:
booster lights and burns for ...sec.
Timer fires a separation charge
booster is now on its own, motor or electronics will deploy chute
Sustainer will then light at the set delay
(not to long that the sustainer looses to much velocity)
Motor or electronics will deploy chute for recovery of sustainer
The type of igniter and power source will have to be tested and you will need to test each igniter to make sure the ohms are the same every time.
One note though, if you are using motor ejection for recovery of the sustainer you will have a lawn dart if you fail to light the motor so I would recommend electronics as primary recovery of the sustainer.