If I missed a detailed description like this that you previously posted I apologize but looking at your response here, you DID need to RSDLite (as you could not access your recovery and did not have a working ROM).
Hmmm...I think you may be right on the one click root methods but I've never actually used them so I can't confirm or deny that. Sounds like you didn't have "full" root privileges. The installation of 1.4 should have replaced your boot animation but I am honestly baffled as to how it would let you put 1.4 on your phone but not allow all files to be copied over.
Once you rooted, how did you install this ROM? Did you use ROM manager or did you do it from Clockwork Recovery?
If you're up for trying it again, here is what I would do. I would Root using the methods listed here:
http://androidforums.com/all-things-root-droid/141116-guide-rooting-2-2-windows-linux.html
Follow this guide cause OMJ has actually gone through and verified all of this information to be accurate (BIG Thanks to OMJ for revamping this guide!).
Something is going wrong for you and I wish I could tell you what is happening...but I just can't. If anyone else has had this problem and found a solution...please post it
Don't give up...it sounds like you have a good understanding of what is going on...just gotta figure out what is giving you issues.