Right, I see now. Listening through your version and the original, the problem is that you're trying to play the bass part, and lead guitar, and rhythm all at once. You've got the lead part (the 9,10,11, 12 -> 2, 3, 4, 5 bit) absolutely right, but to go from that to the Dadd9 is a nightmare as you rightfully determine.
Personally, if I were playing this song, I'd do the verses as you have done, possibly using your thumb over the top edge of the neck to fret the D and G notes on the bottom string. Then, when it comes to the chorus, i'd go back to playing open chords. It'll make it sound bigger, and it'll be lots easier to play. Try just playing the chorus with these chords:
D - 2,3,2,0,X,X
Daddd9 - 0,3, 2, 0, 3, X
G - 3, 0, 0, 0, 2, 3