I can only get deep breath on exhale, forcing a yawn, or reaching down throat. lying down is worse. docs say there's enough co2 in system. what's up?

Your question is not: Clear to me . From what i understand , you have problem of breathing particularly in lying position called orthopnea . The relation between breathing problem and level of co2 is interrelated . If you have shortness of breath due to air way obstruction as in COPD or asthma , your co2 level could be elevated dangerously high and make you confused