asthma and allergies- waking with shotrness of breath

Hello Docs,

I have a question regarding my asthma and allergies. I have been waking up five out of seven mornings with shortness of breath and clear phlegm deep in the lungs.I usually take my puffer around three puffs to open my airway in the morning but the asthma like feeling dose not go away until I get the deep mucus out, the puffer only seems to open the airways to allow me to clear my chest out which usually takes around an hour. I also have allergies to cats and I bought a rabbit for my girlfriend a few Christmases ago. I also been having muscle twitches all over my body for the past few month (driving me crazy) My question to you is could this be due to allergies or maybe an underlying infection or something more sinister like acid reflux? thanks.