Let me respond item by item to expand on what Bob G provided
I have a couple of 66 shelby questions. i'm redoing the original autolite adj shocks. What is a good color match to the original blue paint.
IMHO color is on the lighter side of Corporate Blue though as Bob mentioned a rattle can of that is what others often use. I had the color matched so that is what I use. Would be nice, when I have time, to test different brands of rattle can to an original to see which is closer but that does not help you right this minute
Cameras, monitor settings and so on affect what we see in the following pictures. In my monitor the top row - right side is closer to the right shade. There are some better views in the thread mentioned below.
Another thread discussing the shocks
http://www.concoursmustang.com/forum/index.php?topic=2259.msg11629#msg11629Upper ft shock bushings need to be replaced .Any thoughts?
Couple of places out there that can do it. Some of them have had issues (like many providers) with the current rubber being used by their suppliers that does not seem to hold up well over a fairly short period of time. Have not had them done recently so don't know if the issue has been addressed. Since there are more Mustangs being done maybe some of those owners can report recent success and how long ago they were done.
Was thermostat housing left natural or painted blue?
Hose end had a slip over mask installed at the time the base engine was painted to keep any paint off of the connection surface like the (different engine and application) picture below. Since the housing was unbolted and reused the paint on the bypass hose is typically cracked and the attaching hardware has some paint knocked off of the bolt head.
What are the correct tri y bolts to attach to the engine?
There were a few suppliers of the bolts that held the headers to the cylinder heads. Since you indicate you're doing 6S1102 we'll focus on that period (BTW we own 6S1203). In doing so found (in my limited number of original unrestored examples from around that period) that the sunken head with the circle and tri bars was more likely what was originally used.
The center can often to be found more "sunken" into the head on 66 (non-carry over) versions than what is show in the example to the left in the picture above of examples taken of 65 header bolts. Maybe a change in production, camera angle and or age and wear
Never tested to see what the plating was. Looks allot like bare steel so maybe cad or nothing. These were supplied by the header company with the headers. Use to be packages of these hanging in every hot hod shop in the country since if you didn't check them over enough they could loosen and even fall out
Whats the best thing to use for the undercoating on the firewall some old posts say 3m rattle can undercoating. Is this the best thing to use?
"Best" thing to use. SO far I've not found anything that replicates the original stuff though I have a couple of untried ideas I'm waiting to test. The original product was unlike what we see in later years (example 68 up) and at other assembly plants. According to Ford it was suppose to be an adhesive base and from original examples it had a cobweb effect visible on the finished product. The applicator also didn't normally spot apply but flowed the gun from focus point to the next one. Below is a close up of a few examples. As you can see its part product and part application/technique to get anything similar to original
A couple of examples
More typical heater motor application where the outer two studs are covered and the tool moved under the heater motor and the spray continued. Some was removed during cleaning of the car
A few from cars much closer to your production period
Additional examples can be seen in all the San Jose examples in the unrestored picture threads in that section
Were the gt350 emblems on tail light panel attached with barrel clips?
Sometimes referred to as speed clips. Sure there is a correct technical term for them but the unrestored car shown below should provide you with what your looking for
Hope this helps