You seem to have a whole lot of unspoken assumptions rolled up in there with the phrase 'special creation ocurred'.
There seems no more reason why special creation should allow for the conservation of non-morphologically relevant genes or even non-functional genes than why it should allow for god to put some interesting structures which resemble living organisms into particular geological strata in particular patterns.
You may argue that it is more parsimonious and certainly I would agree that a God who only steps in to kick start abiogenesis might be considered more parsimonious than one who hand crafted every species on the planet and carefully placed them at particular intervals in time and space to make patterns which appear to detail an evolutionary history of nature. But once you have made the giant leap against parsimony of bringing in a supernatural creator it seems penny ante to de-bar him from any particular activity because it would violate Occam's razor even further than one already has.
If special creation occurred, there would be no transitional fossils, for there would have been no evolution.
You are assuming here that transitional fossils could only result from evolution, this is clearly not true if you bring god into the picture. If you allow special creation there is nothing barring the special creation of organisms, or even the direct creation of fossils, which resemble transitional states between other fossils/ organisms.
TTFN,
WK