Hi Bart, The early cars or prototypes, that's only chassis numbers GT101 to GT112, have a lot of variation. Some are open top roadsters, there's differing front ends (as you mentioned, some don't have an opening panel), various add on front spoilers were tried, the first cars didn't even have the rear spoiler, and a load more, including many, many mechanical differences. The name GT40 wasn't even assigned at this stage.
To attempt to clarify........
Simplest thing to get your head around is the production cars, which begin with;
GT40P/1000 onwards = GT40 name officially adopted, (not a nickname as Carroll Shelby claimed in later years, it's on the chassis plate, countless original FAV documentation & forms the first part of the all the Ford Advanced Vehicles part numbers. The nickname rumour gained traction in 2004 with some dim witted Ford press comments about the 'GT' as a 'cover up' for not owning the GT40 trademark !) The 'P' in the chassis number is for production. The numbers run from 1000 up to the 1080's (where we get into one rebuilt, renumbered car & spare chassis's plus continuation cars etc. These are what are usually referred to as the Mark 1's. Supplied new as race or road (street) car specification. There is variation but basically they are very similar 289 V8, ZF transmission, definitive front end (the Le Mans nose), etc. If you look at these cars as a group you'll see a bit more stability in what your seeing. Hopefully ! (Most replicas & continuation cars are Mark 1 style.)
Except !!! Some chassis were modified into Mark 2's for the race program. Higher front fenders, different rear body / engine cover, 7 litre & Ford transmission. Designed for race use only.
GT40/M3/1101 to 1107 = M3 is Mark 3. Built for road use only and available in rhd & lhd (the only genuine lhd derivative). Longer front & rear bodies, the front with four round headlamps (round was required for some states) and the long tail covers an internal luggage compartment (to cook your possessions!). These seven cars often trip up journalists & writers who state 'there were only 7 GT40 road cars', they overlook the thirty plus Mark 1 road cars. The very first GT40 replica kit that I'm aware of was copied off of 1107 by the late Ken Atwell. As the centre section, wheelbase etc is common all it took was for the Mark 1 & 2 front ends and the Mark 2 rear end to be later copied to provide all three variants. Thus a pretty big industry sprung up, several reputable companies have been in business for decades.
The Mk 4 ('the American one' !) is not really a GT40. It's the Mark 2 drive train in a new honeycomb chassis & totally new body style. Built as a race car only & only 8 Mk 4 cars in period, plus another two can am bodied conversions. There are a couple more built on spare chassis & a few continuation cars too. There are (or were) some more affordable Mk4 kits/replicas but they were, like the actual car, rare things.
As you're aware the majority of replicas seem to be Mk 1 style and you can build a copy of an actual team car or the road car spec. Or may be you want to take a more personalised approach. Personally I love a road car 'spec' in a nice period colour, it really shows off the shape.
I've generalised quite a lot & left some bits out, but perhaps you will be able to navigate the maze!
Good luck with what ever you decide to do.
Steve