An overwhelming amount of evidence points to indirect realism being true.
That's an unsupported claim.
This means that all perceptions are spatio-temporally located throughout brain processes.
This, too, is an unsupported claim. Not everyone is a physical reductionist when it comes to mind.
Therefore the body you perceive is an illusory homunculus which actually exists throughout processing in your 'real' brain. There is no problem of infinite regress (ie; who is inside the brain of the homunculus?) because the homuculus or the 'you' is an illusion smeared spatio-temporally throughout your 'real' brains processing.
Similarly, when I look at the house across the street, there exists an "illusory" image of the house somewhere spatio-temporally in my brain, even though the house is larger than my brain. So?
Does the illusory homunculus affect (will, or control) the 'real' body or are we merely marionettes?
What you are really asking here is about free will vs determinism. There's no need to bring in illusory homunculi or marionettes.
If we are marionettes with no control or will over the true body, what would be the evolutionary benefit for the marrionettes existence (even if it is illusory)? How could consciousness be evolutionarily selected if it makes no difference to the organisms survival?
What would lead you to believe that consciousness has been selected, or that it offers any evolutionary benefit? It could just as easily be an epiphenomenon, a "spandrel" (to use Steven Jay Gould's term).
I think this is satisfactory evidence that the illusory homunculus exibits some sort of control over the true body. As if the illusory homunculi that we are, have the role of some sort of control function over our 'real' brains.
What you are therefore claiming is that we possess free will, and that mind has a causal effect on matter. Both of these claims are difficult to reconcile with your initial stipulation of physical reductionism.
I'd suggest you take a look at Raymond Tallis's recent book Aping Mankind: Neuromania, Darwinitis and the Misrepresentation of Humanity which nicely lays out the problems of physical reductionism, and of superficial appeals to evolution.