Metronne, I'm not sure what you mean by "big structural problems". Are they game-breaking? If so, you don't need to rewrite so much as re-structure. Just remember, "There's always a way".
I outline my work in some detail - to the point where I know my plot hangs together and progresses, but still, sometimes, I come up against a problem. One time, I was at a total loss - it just wasn't working - until I remembered something my Sixth Form English Literature teacher (and I'm going way back, here) told me. It was along the lines of "The basis of any worthwhile piece of fiction is character - a writer needs to express and illustrate how the different people in his/her work act and react to their own actions and those of others."
When I hit my "bad patch" I did something which, at first sight, may seem totally outlandish - I wrote a journal for each of my characters - just brief notes, but totally from their point of view. In effect, I had my characters keep a highly personal diary throughout the plot, talking about their actions, reactions and motivations, outlining how they felt about the other characters and what was happening around them.
I suppose what I'm really trying to say is that "character is the key". If you know your characters well enough to determine how they will react to a given set of circumstances, you should be able to find a way through most difficulties with your writing.
There's a great deal said about "story arcs", but, basically, any story is structured by causality - the consequences arising from something someone has done/said/omitted to do etc. When plotting, or constructing your story, bear in mind the need for everything that happens to have a cause - often a previous action - and the need for it to have resulting effects. Things rarely, if ever, happen in isolation, so follow the thread of your story through "cause and effect". A does this, which results in B doing that, which, in turn means that A, or someone else, reacts in a certain way - usually in keeping with his/her character. That way, your story / plot will hang together as a series of causes and effects, fleshed out by your characters' reaction to each changed / changing circumstance.
If you're really stuck, stay away from your work for a number of weeks. Try to forget it and think about other things. You won't, of course. Your subconscious will be constantly churning things over. When you return to the piece, try to approach it as though someone else has written it. Identify the weaknesses (you seem to have done that already) and work out what needs to be done, bearing in mind the two mantras: "Character is the key" and "Causality = credibility".
Best of luck with it.
