I would be careful about determining value of a car that has had its engine swapped. It is a rare find indeed, for a 35+ year-old car to have its original engine/drive train.
I also think it must be clear as to what constitutes a "numbers-matching" car. It is clear that Ford had casting dates on engine blocks, heads, and manifolds, and these are easily read. Also on the block, just below the driver's side head on the front of the engine is the stamped assembly date. Many other engine parts, including the fan, distributor, and carburetor, have specific date codes that identify assembly/build dates.
I think the matching-numbers issue is a bit over done unless you are trying to build/restore an MCA concours car. I've read in this forum that San Jose cars had the VIN number stamped on the block. I have two original San Jose cars and neither has the stamping. My 1966 GT 350 has the VIN stamped on the block on the passenger side next to the pan, and it is well documented that 1965-66 hi-po engines were stamped with the VIN.
At the San Jose assembly plant in 1968, what would be the purpose of stamping the VIN on the block, especially when the VIN can be found in four other places? It seems like it would make it much more difficult and take more time to assemble the car as it rolled along the assembly line.
To be safe, I would check the casting dates and the stamped assembly date to determine the originality of the engine assembly. As to value, leave that up to the buyer.
Just my thoughts on the matter.
Russ