Hey, Bryan...I know it was a very tough decision to make considering all the preparation work that went into such an epic trip. I had to make a similar decision back in 2004 when bad weather and equipment failures caused me to get off the water. I knew I had to get off the water or risk injury/death. I really didn't want to end the trip but heck, here I am prepping for my run to Hudson Bay in 2010 after completing my very enjoyable run from Borden, Saskatchewan to Lake Winnipeg during the summer of 2008.
As others here have stated previously, "better to live for another day to paddle again than take the risk that you might not come back at all". You made the right decision. The health of your body and mind, as you realize, must be in top form when tackling the wilderness or things will start to go wrong that put your life at risk. Equipment failures can be compensated for while your health is good but add more risk if you are struggling with health issues.
I look forward to hearing more about your trip thus far. I am sure you will be chomping at the bit to do it again. This year has been Chapter One. Chapter Two begins when you get going again.

Robert N Pruden