My 3 month old has temp of 99-100 with nasal congestion and occasional retractions and heaving breathing. Does she have pneumonia again?

Possibly. Those are concerning symptoms in a 3month old patient. Pneumonia is one possibility but there are others. These include a viral respiratory illness that is causing wheezing or inflammation in the baby. Regardless these are symptoms that need evaluated immediately either by your physician or local emergency room. It should not wait till tomorrow.
Go see a doctor. A 3 month old having respiratory difficulties and fever should be seen immediately by a doctor. This is particularly true if they have had pneumonia previously. Please do not wait. Hope they are better soon.