Ok where do I start.
1. The gearbox in these cars is the center of the entire design. It is also the hardest design element to change after you have completed the car. The one you decide on will have taken into consideration; power of moror, normal cruse speed you will drive the car, track work and how much and weight of your foot. Power; up to about 375hp the renaults and the audis work fine. Beyond that, up to 550hp, start looking at quafe upgrade for renault and a G50 porsche or beter instead of the audi. More power? the car doesn't need it and you can't afford the gearbox necessary. If you must have 600hp consult a proper racecar builder for advice.
Gearing; freeway speeds around 70 mph need something like a 3.5 to 1 final drive and a overdriven 5th gear at about .8. The R21 renault is right there 3.44 and .87 I think. The most used audis are a little lower geared and 1st is useless in mose people's oinion. Audi final is 3.87. There are other audis floating around even 6 speeds with beter gearing.
Limmited slip; Get a gearbox with one from the beginning. Really! I wish I had. You will have to read up on this A LOT.
Clutch's; it should be without saying that the clutch is going to have take what ever power you want. This can get very detailed at high power outputs above 450hp or so. Ask a lot about this if you build a big motor.
2. Engine;302, big 351 or forget it FE's. The good old 302 will make a solid 400hp. Big 351's up to 427 cubic inch will make all the rest. Check fit. the 351's are 2 inchs taller than a 302. The FE's are no longer necessary and will really complicate things. This should finalized next. You can really spend a lot of money on a motor. Tne truth is these cars will really take as much as the tires you run and the skill you have. But... They work very well on the street with 350hp. The gearbox is a lot cheaper and you will spend more time driving it than fixing it.
My car has a single 4 barrel on it and it works fine. The 8 barrel FI systems really look cool along with the webbers and could be upgraded later with out a lot of loss of money. You can always sell a good old holley and a alum manifold.
3. Suspension; Get very good shocks up front, this will save you some money later and read up on spring rates so that you can only do this once. Ball park for this discussion 300-350 front and 400-450 rear. Good street and track combo. ADJUSTABLE rose joints!!! You need this the first time. Big pain in the ass to reengineer later.
4. Wheels; I like the 17" diameter 8" front 10" rear because there are so many tires to choose from. Mant guys like the 15" diameter because of the orginal car had 15" wheels. What ever you do make sure you understand the tire issue before you buy wheels. Get knock offs, they look cool. This will from doing it later and wasting money on the first set.
5. Air Con. MUST HAVE!!
666. Body work. Oh God what a hassel to do yourself and you will be shocked what it costs to get done. The solution is to ask a lot of questions about this from everbody that has ever owned a GT40. If I was to do another one I would get the kit that has the best body pannel fit, period!
So..... Body fit, gearbox, power and adjustable suspension along with AC. This is the big stuff. If you get these right aveything else will be ok.
All the recomended builders you see in the other posts can do a car with all the above. All of them are currently in business and will do a good job. Its really about what you feel when you go over and check them out. Just like any other business deal. Do your homework and you will be fine.