I have looked over your description and I very sincerely appreciate your honesty. Please don't feel like what I am telling you is destructive criticsm but rather constructive criticism. I know it can be very frustrating to have put all that hard work into your baby and have her sneer back at you that way. I do not feel that it is a serious problem. So don't panic!
In between the comments I make if you could make your own notes in your reply to me on the particular points so we can gradually narrow down the source of your scratches.
I washed the car using Dove, which I was told would remove the wax without hurting the paint then Meguiar's Crystal wash.
Note to self: Don't get side tracked here! Although it is so difficult to keep from going on a rant right about now. Grrr! I have some other posts on here regarding surface prep under "My Car Care Philosophy" that I think should be read right about now.
Then I used a mothers claybar with their liquid detailer as a lub, which is what the directions recommended
Excellent clay bar. However, was the car 100% dry when you clayed it? I know some people like the car to be wet when they clay, and perhaps I am way too anal but what I have found after claying probably 1,000 cars myself is two things:
Sometimes I miss a spot when I am washing and when I go to dry the car I notice the area and I need to wash that area again. So I am saying that you may have missed a tiny area on your car and some of the dirt got trapped in your clay bar and you rubbed it into your paint.
Another thing is that water is attraced to other water. Ever notice 2 beads of water close together and they seem magnatized and the two join to form a bigger one? Well, the same thing can happen when you are claying but in a slightly different way. When you spray on the surface lubrication near a badge, piece of body molding or piece of trim the piece of dirt that is hiding in the water under the badge can get drawn out and trapped in your clay and ground into the paint.
Some people have good results with their method but they fail to realize that there are people out there who have not clayed before and pass on their short cut and that is where problems can occur.
Meguiar's chemicals 1, 2, 3 (paint cleaner, polish, and canabara wax times 2) all following the directions on the bottles.
I tell people all the time not to polish unless they absolutly need to and this is why. What sort of applicator did you apply the poish with?
I used terrycloth cotton towels I bought from Autozone.
I think this could be where part of your problem comes from as well. Those towels probably aren't 100% cotton. 100% of the cotton they used was 100% cotton but they probably used some sort of cotton/poly blend. That said, did you wash and dry them before you used them? If not they are often brittle and can scratch paint.
So the process was wash the car to remove the wax, I did this twice, then put the car in the garage
I am sure you removed all the dirt so that is not a concern now. However did you leave your vette wet as you clayed?
spent a few hours using the claybar, which I would first spray the lub on the car in an area the size of 2 feet by 2 feet. I then rubbed the bar back and forth listening for noises of stuff being picked up by the claybar. When I could feel no more pulling and no more noise I moved on to another area.
I actually find claying to be theraputic. I was nervous the first time too. Were you wiping it dry when you finished the section?
The cars paint had sort of a flat look at this point. Not much gloss.
Hmmmm, clay should not dull it. Perhaps the Dove washing had some sort of adverse reaction to the paint and it was revealed afterward. Torch red is clear coated for that year, correct?
Then I put the Meguiar's paint cleaner on it, and rubbed it in in circles, let it dry for a few minutes and then wiped with a terrycloth.
Ohhhh nooooo! Not circles. I blew out my shoulder (2 times total now) several years ago and had to switch from circular motions to side-to-side and up-and-down motions. I found that it made a huge difference in the amount of surface scratching. A lot of companies now suggest this too because of the way the sunlight gets refracted to the side and not in various directions (aka the swirls you are referring to). Plus you removed a dry product with a brittle towel. I know your name is Jedi, but I hope you didn't apply too much force when rubbing the product off!
Then did the same with the polish
Same answer as above. Plus the addition of the abrasives in the polish added to the eventual result.
and then the canabara wax twice.
I don't think you can get depth with that series. My suggestion is switching over to Meguiar's #26.
The car looked a little bit duller then when I first bought it but I figured I could fix that when it got warmer during the spring and could spend more time on the paint. Now I see swirl marks, and these straight lines when the light hits it just right. Anu suggestions would be greatly appreciated.
I'll make a few suggestions once you have replied to the questions and suppositions I made.
But I did not rub too hard, I knew ahead of time to be careful with this and the polish due to the abrasives. 
4LT GS Roadster
