I was the same way, poor quality sleep, waking up with lots of congestion, taking a long time to "clear" my head each morning. With testing I found allergy to dust mites and other things.
What has helped me, as the others have suggested, is to keep a dust-free as possible room, wash the sheets more often. High quality American made products can be found at this site, it's the one my holistic doctor recommended:
http://www.natlallergy.com
Their mattress and pillow covers protect from the mites, bedbugs and pet dander. I have since covered our pillows, mattress, boxspring and comforter. I also invested in an air purifier which the doc said to turn on three hours before bed and leave on all night. I don't always turn it on beforehand.
These changes, which I made in financial baby steps, have made a huge difference for me. I hope this helps.