I would say it depends on the complexity of the organ it should replace,
if it is a relatively simple organ, say a heart which is essentially an electrically driven pump, it would seem logical to replace this with a mechanical counterpart, I would think wrath of iron gives us a nice example of this.
Regarding the eye, since it is in principle a system shaping and partially processing a light field, this should also be simple to replace,
human nerves should also be rather simple to replace by a fiber like technology greatly increasing the response speed (I guess power armor already does this).
Regarding strength, I guess the PA is the limiting factor.
More complex organs on the other hand like special glands, that is another thing to replace these, and probably it is by far not efficient to do this, furthermore the SM body should be the ultimate in genetic engineering.
I agree with MECinq that certainly the autorepair functionality is nearly unreplacable, as is the adaptivity of biological engineering (nids vs necrons ?),
As such I would say it depends on the funcionality but besides some simple processes, it does not seem logical to replace everything (mmh an IH would shoot me for this, but he would probably anyway so screw him)