Your won't have any problems with that short shaft as your boat being a deep Vee compensates for the shaft length.
Your main problem will be clearance steering with the main motor interfering. May want to consider a connector bar between the two motors & then use the steering wheel when running the 9.9 instead of trying to steer it with the tiller, unless you cut some of the transom out to slide the kicker sideways for more clearance.
You stole the motor, in my area it would be worth double what you paid.