nitpick on shrinking that's always bugged me:
A virus is very, very small. A germ looks like a 2 mile long asteroid compared to the size of a typical virus.
Now, we assume that the shrunken kids have the same metabolic requirements, and are made of the same number of atoms while shrunk. Gotta obey conservation of mass and energy after all. A good deal of an atom is vacant space, so if we reduce the amount of vacant space and instead concentrate charges.... whoop-- we just did some crazyness to the kids's biochemistry on accident! By altering the charge gradients from the shrinking, we just changed the energy needed to make and break bonds between the compressed atoms... sorry kids, didnt mean to cause horrific problems like that!
Ok, so maybe we use magic to protect the kids from the outside environment, shrink thier atoms like before, but we use even more magic to balance or slightly cancel out the now increased bond energies so that the kids dont instantly undergo horrible chemical reactions inside thier bodies... oh no! they are suffocating! Guess we didnt consider that the non-magicized oxygen that we expected them to be breathing was not being magicized, and thus had very different bonding properties compared to the magicized atoms in thier lungs!
OK, let's give them magicized scuba gear too. Oh good, they can breathe! but they cant swim! the magic protecting them from interactions with the inflated atoms around them prevents traction!
Better re-inflate them and see how we can do better.. OMG, what's happening to the patient we put them in!? He's swelling up like a baloon! OMG! its the air the kids were breathing that was magically shrunk in the tank, suddenly reverting to normal volume inside the patient!!!
the simple side of it: shrinking and inserting macro organisms inside a living person is just plain silly, and dangerous, if it were actually possible.