Does the equivalence principle imply that there is some fundamental difference between acceleration due to gravity and acceleration by other means (because there is no way to 'feel' free fall acceleration for a uniform gravitational field)?
Does General Relativity allow you to describe the acceleration due to gravity without Newton's second law (because every other source of 'push or pull' outside the nucleus involves the electromagnetic field)?
Is the acceleration due to gravity a result of changes in time dilation/length contraction as opposed to an actual push or pull?
General relativity attributes gravitational effects to the curvature of spacetime. Free objects tend to move along paths which minimize the energy required. The presence of massive objects alters the curvature of spacetime and so affects observed motion.
When an object is subjected to a force which counteracts it's ability to "fall freely" it feels a fictitious force that we call gravity. For example we feel the fictitious force of gravity, because electromagnetism is preventing us from freely falling towards the Earth's core.
Now from a classical perspective this fictitious force must have an associated acceleration due to Newton's second law. We call this the "acceleration due to gravity". But from the point of view of general relativity this acceleration is just a frame dependent quantity.
So to answer your questions:
Yes - quite right. Acceleration due to gravity is an effect we observe from a non-freely-falling frame like Earth's surface. It's just an artifact of our choice of reference frame. Acceleration due to other forces (principally electromagnetism) is frame-independent, and is therefore a genuine physical effect.
No - the classical concept of "acceleration due to gravity" is necessarily tied up with Newtonian ideas in our reference frame on Earth's surface. In general relativity we generalize our notion of acceleration to 4-acceleration. One then calculates the motion of particles through spacetime by setting this equal to zero. So heuristically the equation of motion under gravity $mg=F=mA$ becomes $mA = 0$ in general relativity.
Yes - ish. Time dilation and length contraction are effects that one experiences when comparing different frames of reference. And we've seen above that "acceleration due to gravity" is also just a frame dependent effect. But it's not really true to say that one is a "result" of the other. It's better to realize that time, length and "gravitational force" are all frame dependent quantities.
The equivalency principle relates being accelerated to STANDING on a massive body (not free falling toward it), and that the acceleration force felt by an observer is directly related to the amount of gravity of the massive body the observer is standing on. Free falling toward a massive body in this context is equivalent to experiencing no acceleration at all, and an accelerometer would record zero acceleration in free fall.