Good choice of song! I Asked about the very same passage to my piano teacher, and it's actually not as difficult as you might imagine.
Ok, here goes. Notice that the beginning arpeggios are all just a D major, and you have the exact same shape on the keys for each chord. I don't know what fingering you are using, but if you take 3 notes per hand(ignoring the low D octave for a moment) you have the pattern Left,Right,Left, and then one note with the right hand at the top.
The key to practicing these arpeggios is to practice the chord shapes, and shifting positions. So set your metronome up at a slooooooooooow speed, and practice shifting chords, making sure that all fingers are in place before you play each chord. You don't need to do this to play with single note at slow speeds, because your fingers can compensate for not being in position while other notes of the same chunk are being played. With that in mind, at fast speeds your fingers do not have time to adjust, and so when they aren't ready on the key they will let you down and ruin your flow, as you mentioned in your question.
When overlapping hands I believe you always go over, but I could be wrong. The answer is most likely do what is most comfortable. So in this case it'll go left over right, right underneath to play the top note, Right over left on the way down, left underneath and then you're on to the next shape.
As far as the timing goes,I don't believe this passage is to be played strictly, but if you want to learn about the fun fun world of quintuplets and septuplets then this wiki is a nice place to start :)
Hope that helps!