I talked with my a physics professor and I think (hope) I got the anwser to my question. First of all, I was always given:
m_1 v_1 = (M_2 + m_1 ) V_f,
the problem that was hanging me up was how to derive this function, the reason being that nowhere in the momentum equation is the two masses combined, its always derived based on the principle that when the two masses hit, they both go off or one goes off for that matter, but they BOTH go somwhere, so you always have the sum of the product m_1 v_1f + m_2 v_2f on the other side of the equation. I think I got the equation correct by saying that if they both move together in the end, then I can think of both masses moving with the same velocity, both magnitude and direction. so then I would get,
m_1 v_1_i + m_2 v_2_i = m_1 v_f + m_2 v_f. But since they both have the same value for the final velocity, then we can group the masses together, and we get, the basic momentum equation for inelastic collisions.
m_1 v_1 + m_2 v_2= (m_1 + M_2) V_f. Its kind of obvious and stupidly simple now that I got the equation, but I just wondered how to get it, becuase in my book were just told that " because momentum is conserved it is equal before and after". As a consequence of the way I did it, could I also think of the system as "technically" not being physically connected, meerly they could be side by side, without actually being tied together, and move with the same velocity. They would be in physical contact at some point, forever and ever, but not in the classical textbook sense of a thing of putty being stuck onto some other object.
My second problem was another basic property of momentum I carelessly forgot. What Kept getting me caught up was the fact that I said to myself, as this bullet goes into the pendulum, its going to continually transfer momentum as long as its moving inside the block. So why can we just say it conserved momentum using that equation I described above, and why would it not be some integral of the momentum vectors from the point of contact until the point of being stuck and stopped inside the block. I think the reason we can just use the conservation of momentum at one point is that if we conserve the total momentum, just limiting ourselves to the case where it strikes the block, it would yeild the same result. I could transfer momentum piece by piece from the point of contact until the point it stops, OR, I could transfer ALL of that momentum in one shot, assuming that happens just at the point of contact. I guess in that sense, it would be as if the bullet hits the front of the block, stops dead, transfers all of its momemtum, and the system as a whole moves. Oppositely, I could picture it as what really happens, and that would be that the bullet hits the block, and slows down on the way into the block, and in the process, the block and bullet continually go up to speed with time. In the case where its all at that single instant, I guess it would be like saying right at impact it just goes to that slower speed of the block + bullet system at once. ( is that logic correct?)