The whole point was to allow them to escape with the princess, run to the rebel base on Yavin IV and KB it. But as we all know things did not go according to plan.

I knew that would come up.
They didn't know that Han, Luke, Chewie, and Obi-Wan were hiding in the secret compartments. I am assuming that the tracking device was put on the Falcon AFTER they realized that they had been infiltrated.

Also how does the Rebellion steal an Imperial shuttle and nobody realizes it. I mean when the shuttle transmitted it's ID to the star destroyer it should have come up as stolen. It apparently had been in rebel hands for some time since it had an older authentication code.

Yes their security sucks.

How about having a tractor control power junction with no security lockouts whatsoever?

As I recall the shuttle didn't transmit its ID it trasmitted a code.  As in they had an old, but still acceptable word of the day.

And I'm sure somebody realized that the shuttle was missing, but they had to have hundreds of thousands of the things.  It would be similar to an HUMVEE being missing.  Sure somebody would know that it's gone but the whole military wouldn't be be on the lookout.

Good analogy.

Emperor wanted them at Endor to crush the Rebellion once an for all.

Even if they could get their security in order they don't have the sensors to stop Federation infiltration, much less someone extra sneaky like the Dominion or Romulans.  A presumably elite Star Destroyer could not detect the Falcon when it was attached to the ass end, or in the asteroid field.  Federation ships can detect minute radiation several star systems away at high warp (ST Nemisis, positronic emissions).  No way they can stop infiltrators with space-WMDs.    
 

You are correct.  I did kind of discounted the incredible Federation sensors that are able to detect something that is happening at that moment light years away.  (INCREDIBLE, adjective: too extraordinary and improbable to be believed)

And to be frank why would you have a bunch of sensors monitoring the skin of the ship?  What's the purpose that would cause the starship customer to levy the ability to scan the surface of your own vessel as a requirement to the manufacturer?  Our Aegis cruisers are able to see and shoot objects from the surface of the water up into space but wouldn't be able to see a guy hanging from the fantail.

I'd put Star Treks Sensors in the plot device category. Giving your star ships god like omnipotent vision has it's advantages.