If she has low tone/floppy baby syndrome I hope that your doctor has run a full gammut of tests. You should have seen a developmental pedi, and also a nerologist, as well as your therapists. There are many different reasons for low tone/ floppy baby syndrome. They key is to find the underlying cause for early treatment.
L cartinine deficiency is one reason for low weight and low tone. You could have the doc check her. Give a diet rich in med chain triglycerides (raw virgin coconut oil, or palm kernel oil, butter) and low in long chain triglycerides (canola oil, corn, veg, etc)You can feed coconut oil straight from the tablespooon, cook your pancakes in it, etc.
Put chia seeds in her pancakes. Look up the health effects of chia seeds online.
Choline deficiency should be looked at too. (folic acid deficiency will affect choline levels).
Fumerase deficiency can cause poor feeding, hypotonia and failure to thrive. it is rare but it is possible.
cobalamin deficiency is a curable metabolic disorder. Suspect if there is physcomotor regression after 6th month, to hypotonia(severe) by 12th month.
Certainly other vitamin deficiencies should be considered and explored. Lack of Vit b3 can cause lack of appetite, b6-weak muscles, b1-anorexia/weight loss, weak muscles. Since b vitamins work together, a full b complex vitamin should be taken, in liquid form, under the tounge for quick absorption. Benfotiamine is a fat soluable b1 that can be taken orally , maybe you could add that to the b complex. Consult your doctor.
Vit A deficiecy can cause a lack of appetite. Vit A is also good for bone development. Cod liver oil has BOTH highest levels of vit A, plus the vit D in it too. Buy high quality Carlson cod liver oil- (found online if you cant find it local). A bitter taste to cod liver oil means it has oxidized. Keep it in a cool dark place and use it up within 6 months.Throw it out after that.
Magnesium is another one that if deficient in, can create a large host of different problems. Magnesium is a chemical gate blocker for nerves. It helps muscle tone. It helps calcium harden the bone. Magnesium can be absorbed thru the skin by spraying on "magnesium oil" and letting it dry. Also "Nature calm" is a drinkable form.
So bottom line I would highly consider cod liver oil, b complex, and magnesium, if nothing else. They are all safe. Again consult doctor.
Other reasons for low tone could be hypothyroidism. (very prevalent in children on SOY formulas and soy in diet). Coconut oil should help with this as well, it is progesterone protective.Progesterone balances estrogen, and estrogen disruption causes thyroid problems.
celiacs/gluten intolerance (hopefully they have checked her for this already), and if a baby under 6 mo has had
low tone with the poor feeding and weak cry- botulism should be tested for. Vaccine reactions, other infections such as Gullian barr, meningitis, polimeylitis, sepsis, Myasthenia gravis. I have read reports by some physicians and scientists who claim that other bacterial infections from mycoplasma or spirochettes have been suspect in failure to thrive (poor feeding and low weight).
ps... you didnt say if she has any problems swallowing or not that may contribute. Problems swallowing , or choking on food, can be a sign of iron deficiency anemia or magnesium deficiency.