Now that we know the Engine isn't original, then what else is different?
My brother provided me this diagram of the engine (thank you very much), identifying polarity, the starter solenoid, and the alternator.
Not having a generator seems to indicate that the alternator is period with the engine block.
My brother also tried to use the fuel pump on his period correct '67 MK3, it didn't fit so it is also puts the fuel pump in line with the engine.
The SU 'HS2' Series Carburetor is period of the car, not the engine.
The fan definitely is from the later model engine as it isn't metal, and it has more blades than the original fan.
The exhaust manifold is a mess. From my inspection it appears to be period correct for a '69 Spitfire. It's corroded and has a patch held together by a bolt, welded in place. Also, where it connects to the exhaust pipe, the threaded inserts have been replaced with bolts through and through. It also has a piece cracked off at one of these bolts, though not so much so as to leak.
On the shelf next to the master cylinders, there is a mount system for some missing piece, with broken plastic pieces still left in the mount. I have no idea what was here or what someone would mount here. Please let me know if you have a guess or know what was here.