When I get back into physical exercise aftera hiatus, it takes me a few weeks to build up the respiratory endurance back to "normal" levels. My cardio is running, so I'll run for a 1/4 mile, walk a 100 yards or so, run another 1/4 mile, walk, etc, etc. After a few weeks of that, the walking has been reduced to a cool down post run.
You may want to see a physician about your issues, if you've not already.