Brett,
A word of advice, using anything other than the supplied Canon software for RAW conversion and editing is bound to end in a disaster. Canon's RAW format is proprietary. Everything else is reverse engineered. And, as you've no doubt discovered, gives less than acceptable results. You've spent a decent amount of cash on your gear and shouldn't expect anything less than what your sensor has recorded.
I won't mention my thoughts on HDR as they're well known and will get me into trouble.
All the best.
H