Side-kicks:
Why not use a boxing paw? In a similar way you may use it to throw a hook or high-kick.
It is enough soft from the opposite side to prevent damage to the head of your partner (especially if he is in a helmet) - and enough big to protect the head.
Of course, your target is small enough - as you want to target a neck, you may strike to the bottom of paw - but that is!
Front-kicks:
For front-kicks to the neck - the general approach for kicks may be applied. As all what you want is to kick into a generally small target - just try to aim and hit. The problem you specified is the distance - as long as neck is a bit inward, kick distance should obviously be a bit more longer. But..
If your problem is in distance measuring - then try to train with a rope. Really, that helps me - especially with roundhouse kicks (ushira-geri, if more concretely).
Rope judges you realy well. In both distance and targeting (for targeting, you may just mark rope at some height with some another, colored small rope). In fact, it is an ultimate judge (and that is cool!). When training with a bag, you may hit it only a bit, or just touch it and not really hit. But for the rope - there are only two options - you hit or you miss. So, rope prevents anybody from freebie-training.
So, general answer, I think is to improve your distance sence - and for that - rope is really best you may do.