Lawman9: "The San Shin No Kata are something you should be practicing everyday. They teach you the balance, distance, and timing needed to perform everything in the Kihon Happo. They are just as important."
That summed it up quite nicely, I will elaborate just a little.
Mon Mon: "What is the primary difference between the Kihon Happo and San shin no kata?"
The kihon happo are the fundamental starting point forms for bujinkan taijutsu. They teach a variety of basic evasion, blocking (i.e. counter-striking / receiving methods), striking, grappling, and throwing maneuvers.
The sanshin are more of a combination moving meditation / body integration set of movements. The sanshin are almost always practiced solo and teach the balance and coordination aspects of bujinkan taijutsu, as well as how to move naturally in a relaxed way to generate power. They also, to an extent, teach different strategies - chi: holding your ground; being direct, sui: receiving and flowing, ka: attacking forcefully, fu: evasion, ku: distraction; using combination attacks.
As lawman stated, sanshin should be practiced everyday - it is something that you can do easily on your own at home, and getting better at doing sanshin helps you perform better at every other technique in the bujinkan.
The kihon happo should also be practiced often, but not necessarily every day, or every training session. They must (in my opinion) be practiced in paired kata, so you can't really do them on your own. The kihon happo also contain more grappling than striking forms, while the sanshin only teaches striking methods.
Practice both as often as you can along with plenty of ukemi skills and weapons-familiarity and you'll have everything you need to begin learning bujinkan taijutsu.
