Good morning Gaz, and welcome back after 11 years!
I can tell you that #003 is known the Two-Sixties, having been owned by a member in the past. There is not a lot of information, except in private 'Member only' postings, but I can't see anything untoward being said, apart from the fact that it is a bit 'quirky' being a very early production car. The clutch you have noted, but some other things are fairly unique to cars up to #027, the first SERIES production car. Nothing to worry about, but different.
Numbers #002 to#026 are not technically prototypes, rather early production development cars, not intended for sale to the general public. Fully type-approved Production cars, but not made on the production-line as such. Some were used as press cars, sales training vehicles, and some as MGR Director's/Management cars etc. Eventually in fact, the majority of them did 'escape'. The specific role of #003 is unclear though, if indeed it had a planned role at all. It certainly wasn't a crash test car !! The fact that it is a very early car should not negatively influence its market value in my opinion. In fact, an early LHD sibling, #012, is for sale in France for about £40,000 at present!
I wouldn't let that put me off personally, and I would take a look, but that is only my personal assessment.
David