I think it was in the late 1990s that the entire rail system was rebuilt with new rails and ties and it looked very nice. Then it was decided to mothball the railroad. I visited in Sep-Oct 2000 and the tracks looked great, but not used. Not too long thereafter the tracks came up, and during subsequent visits it was clear the Navy had done a great job of obliterating the railroad, scooping up the ballast and repaving the former grade crossings. You could no longer tell where the enginehouse had stood.
A fairly limited amount of track was left in place as a spur off of CSX but it appears to have been axed. While largely in place, you can clearly see in Google Earth that the switch is gone.
Three of the Yorktown GE centercabs were loaded onto flats and shipped to Yermo Annex of Marine Corps Logistics Base Barstow, CA, which had no use for them. Eventually they were sold to Larry's Truck & Electric in McDonald, OH. At Yermo Annex I met two LTE employees loading and tying down the locomotives onto TTX flats for shipment to McDonald.
I heard about Reading cars being there but never saw them myself.