Ok, you are extremely fortunate to find a 997 in such a good condition. To answer some of your queries:- the 12 A 183 cylinder head is the rather less common variety fitted to the 997 and is original to it. Unfortunately there is a 1071 Cooper S head with exactly the same number! The difference back then was identified by giving the Cooper S head a colour mark (I can't remember exactly which colour, either white or blue I think). The two heads are completely different. A classic piece of BMC confusion that has bothered enthusiasts for years.
The heater valve is correct. I am assuming you have a simple heater in the car, which is a very square box with a flap that pulls out? Fresh air heaters (rare) have trunking and a snail shaped blower in the engine bay and a large rectangular box for the heater.
It sounds like the part missing from the clutch cover is the slave cylinder, but a photo would be needed to confirm.
The rocker cover is correct and a rare part very often missing. The difference with other rocker covers is the angle of the breather pipe.
As for the reg, my own 997 is 939 ACE and as the 997 Coopers were being built before pre fixed regs came in 3 numbers and 3 letters are not uncommon. Sorry I just noticed that you said 2 numbers and three letters, which is a tad unusual.
I would suggest that you visit the Mini Cooper Register website
www.minicooper.org The guys on there have a considerable wealth of knowledge and will be able to help you.
Edited by ace01, 10 January 2012 - 10:32 AM.