Ok, I could quote all of that, and pick it apart, but it's easier to just list the breakdowns.
64 road cars - these are F1 road cars built for customers from late 1993 to mid 1998 and that number doesn't include the XPs.
28 GTRs - 9 '95 GTRs, 9 '96 GTRs, 10 '97 long tail GTRs. The Ueno Replica was the last of the '95s, #09R.
5 F1 LMs - these are the customer LMs - two of which are black. A total of three including the black ones went to the Sultan, one of the other two is now in the US and the final one is in Japan.
2 F1 GTs - these are the customer GTs. The black one went to Brunei, the Burgundy one to the LM customer in Japan.
Those numbers in bold add up to 99 F1s. That's one shy of the magic number 100 so obviously McLaren Cars decided to roll '56XPGT' into the tally to get their even number.
Then, as you mentioned, that leaves 'XP1 LM' and the 5 XP's road car prototypes (XP1 - XP5) unaccounted for. Add them to the previous '100' and now you have 106 McLaren F1s produced. Then add the spare chassis, which was built, but I do not believe has been used at all anymore, and that brings us to the often quoted number '107'.
The Clinic Model should not be counted as it's not even a true chassis. It was built by a prototyping company called MGA and it's construction would not be the same as the production F1s. Remember it was built in early 1992 and the first running prototype 'XP1' wasn't built until late in 1992. The Clinic Model also was not a runner, meaning it lacked the proper drivetrain components and I'd assume things like the suspension weren't completed either. Think of it as a 1:1 scale model if anything. It should never be included in total number of F1s produced. I even think including the spare chassis is somewhat misleading.
That's it - that's the total chassis history of the McLaren F1. There are no extra cars popping out of the woodwork, just some mysteries being solved here about which car was which. For instance, we used to believe that the West Adrenaline GTR was #09R since no one really knew about the Ueno replica that was built for the Sultan. Now we know that info was incorrect and will have to pursue the real chassis number for the West car - #04R is a good suspect given the evidence. Also, it had been reported that the JGTC Hitotsuyama Racing GTR had been built up from spare parts which led many to believe, including myself, that the spare chassis had been put to use and that there were really 29 GTRs total. Now given new evidence, it would appear that GTR #25R was actually rebuilt using spare parts in order to make it whole again for the Hitotsuyama team. No more mystery GTR...
Anyway - hopefully that sleep deprived rambling will clear up some of the confusion you are having. Don't you have a copy of the 'bible' by the way? I thought you did?
>8^)
ER