Thanks for the encouragement guys.

Today, the sun rose and the lights came on again. And with that also a flash of insight in which I saw the root to my problem. My ear was not transcribing the song as well as it should, so with the chords a tad off, it just seemed like all hell was breaking loose. So this morning, in the light of a new day, I went to:

http://www.onlinesheetmusic.com/

And with this excellent resource I was able to get the actual sheet music - what a help it was. In past two hours I have made more progress in laying out this song then the past 2 days. My RT bass player is now all of sudden sounding much better (hehe).