So after practicing my chord progressions pretty hardcore the past few months, I'm now learning that all progressions - even complex ones - need a harmonic goal. It makes sense, as this give a sense of direction to where the melody is going.

My question is: what are some good ways to shorten up a more complex/longer chord progression, or provide harmonic mini-goals throughout the progression?

I think I understand your question, but please correct me if I seem to have missed the point. This is an unusually specific question for song writing...

I would divide the entire thing up into sections that make sense either mathematically or musically. Know that at the end of each of these sections you need to basically achieve a kind of pleasing cadence, so be aware of what your final pitch is going to be. Come up with short melodic lines to achieve that, (I would probably be thinking modally - ie, if I had a section ending in a II chord, I would probably be thinking of what would be a pleasing end to a Dorian phrase).
Leave breathing space between each section as well, don't feel like you MUST play every beat, less is usually more. Having space will also allow ideas to make a little more sense as separate entities.

Has that helped in the slightest?