Hi Dave;
The Merlin that was originally in N13Y for the Thompson race was a Merlin 225. We had a 224 for it just to hang the prop on because the engine disappeared back in the day when it was sent out for overhaul. There was no engine when we got it as Len Tanner had bought the aircraft just for the Merlin that was in it at the time. I don't think I can comment on anything specific at the moment, because it's third hand, but through some recent, fortuitous, meetings with people and some dealings, they think they have a 225 for the aircraft, and the mods done to this 225 engine are strange. No one has seen them before, so it just might be that the original 225 has returned home, though not for sure yet. Johnson apparently had some mods done to move the chin scoop and mount the skins. They are currently looking into to it.
There are a lot of little things missing, including some of the attach fittings for the fuselage to the wings. The landing gear was gone, and it appears as though the horizontal might not be original to N13Y.
In a side note, you asked about the old storage area and the DC-3, the photo below was from 1970 and shows the location of the storage facility and the current location of the air museum. You can see all the small buildings and each one was stuffed to the gills with stuff! I marked the PBY so you can get an idea. there are other airframes there, but they are had to see in the original photo due to the resolution.

Hope that helps a bit!
Jerry