Hi Dan -
To my knowledge Dr. Lee never wrote a manual for the firmware. I believe the document you have is the most complete document that there is. The rest of the info I have found in various blog posts on Dr. Lee's KD8CEC blog - http://www.hamskey.com/ and right here on the forum. He hasn't posted in a while but in the past he has been responded to questions. I learned about the CW offset from the posts on here and then on his blog. I've also poked around in the firmware source a bit.