I don't do Pinan actively but anyway in reference to kakushite's comments:
Firstly, youtube would be the last place i'd look for good Karate videos. Of course there are good videos of Aikido, BJJ, etc., these are arts with far more cohesion in terms of organization than Karate has..generally speaking.
Repetitions in Kata often don't carry a direct meaning, you can find one, but they aren't meant to be a literal stringing of techniques much of the time IMO, so looking for meaning like "why are there three" isn't really something that has an answer.
Far as the techniques themselves many are really simple, shuto is a really obvious one - a wedge. Wanna do it in a 'sequence'? have uke keep punching and keep wedging/striking him lol, try inside and outside the arm..there's your sequence. Always adhere to KISS (harder to do IMO if you go groping around for "sequences")rule and focus on stuff that actually functions instead of what "should" be there.
I am a kata enthusiast and I believe there are a variety of good self-defense sequences in Pinan. But it is my opinion that much of what passes for bunkai is just bunk. I would be grateful if anyone would point to youtube videos that show full directional sequences as self-defense applications.
No it's not on youtube, but you can check out Ian Abernethy's site for instance, and he also puts out videos for free periodically, as well as free articles. Wilder and Kane's Way of Kata is great on this subject, there really is a huge amount of information out there if you look in the right places. Most of what is on youtube in terms of bunkai is pretty bad, I wouldn't bother with it. Alot of the things you bring up about kata, such as seemingly not protecting the head, seemingly countering to the body, etc. have been answered by the people above..honestly if you are interested in the information send me a PM and I can give suggestions.
As far as 'full sequences' check out Taira Sensei's Goju stuff. Personally I don't see why anyone needs 'full sequences', but Taira's stuff looks fantastic and it's flow drill type material.
Here's a couple questions for you:
Do you honestly think that the kata designers thought it was a good idea to not protect the head? Do you honestly think the kata designers didn't know it's effective to punch to the head?
If the answer to either question is no, then possibly you are just looking at them wrong?
This forum, as well as others often have posters make claims that kata are complete empty hand fighting systems, that the movements can all be used in useful ways.
What do you want someone to actually describe exactly what they do for you? Geez man, check the sources I mentioned, this stuff is out there, and it ain't that hard to find.