Hi Kathylee , welcome to Mumsnet. Obviously I can't say what is happening with your ds, but I can tell you my experiences. Dd1 was born also with pulmonary stenosis and an atrial septal defect, as well as hydrocephalus . She was developmentally delayed too, didn't crawl until she was 15 months, and walked just after her 2nd birthday. She was lucky and managed to avoid an op for her heart, despite being told she would need one, as it healed up on it's own, but like your ds she still has a slight murmur, although it makes not difference to her lifestyle (she's 11 now). She also managed to overcome her hydrocephalus and developmental delay, and is on a par with her peers, with in fact a high iq (not that she shows it sometimes!). A swollen heart is not only a sign of Downs Syndrome, as dd had this when she was only a few months old. It can be due to many reasons. I was told that her heart would always be like that, but tbh if it still is it hasn't hindered her at all, apart from being quite sweaty when she was younger.
My fourth baby (and my youngest)is now 2 and he was diagnosed with cp last july aged about 161 months, although I had a feeling he had it from much younger. He is borderline moderate/severe, and like you has physio every week. He is still unable to sit properly unsupported and definitely couldn't be left unattended. He can roll over, but he leads with his head rather than his legs, he commando crawls, and can bunny hop on all fours once or twice before giving up. He has no standing balance and cannot walk. My son is a spastic diplegic, affecting his legs, which are every tight, but he is also low tone in his trunk, which causes him to curl over, leaving him with a curved back. He also has a squint and wears glasses, another side effect of the muscle tone and cp.
There is often a dispute between developmental delay and cp especially if the symptoms are mild, as the two can be so similar. In fact some docs now like to call cp global developmental delay. Personally I disagree as it infers that cp is something that could get better. It might also be useful to know that children with cp often show signs of white matter (brain damage) on mri scans, BUT not always. If a scan looks ok it doesn't always rule out cp, but white matter means it definitely is. Cerebral palsy is quite hard to diagnose because it is so different in each child. One can show massive signs of brain damage and have hardly any symptoms, and others (like my son) can have mild brain damage and big repercussions.
I would suggest keeping up the physiotherapy, as it will help him regardless of his diagnosis, and possibly asking for a second opinion , get him referred to a paediatric neurologist, and ask for the mri results to be looked at again.
I hope this is helpful to you, and haven't sent you to sleep! Good luck.