Have you tried Enfamil's toddler formula? Enfagrow Premium provides a lot of the vitamins your daughter needs to keep her immune system strong - vitamin c, vitamin d, prebiotics, etc. There are other ways to get her these vitamins, but I've found this to be easy for my son. He loves the chocolate flavor. It does contain milk though so if she has a milk allergy, this might not be a good idea.
Is she still following the diet prescribed by the naturopath? If not, get her back on it. Grains and dairy can cause a lot of problems so you could try cutting those out and see how she does. Eggs and nuts can cause problems too. I know, what's left? Fruits, vegetables, meat and fish - give it 30 days with a variety of these foods and see how she does. Then you can start adding one thing at a time back into her diet to see if they cause any problems.
Also, please please please get off the antibiotics and don't use antibacterial soaps! Plain old soap and water is all you need for your hands and your household cleaners. The exception to this being if that pesky MRSA won't go away. With that, she'll probably need a cocktail of strong antibiotics by IV for a while. Hopefully it's gone though. Those drug-resistant bacteria are scary!
Finally, one last thing to try for the colds and ear infections. I just read this morning that putting a capful of a 3% hydrogen peroxide solution that you can buy at the pharmacy in each ear helps. Pour the small capful (may want to use a dropper instead of the cap for a toddler) into the ear, let it bubble and then drain into a towel. Repeat on the other side.
Good luck! It's heartbreaking to see your kid so sick! :(