Time for an update........
Cylinders came back from Gast so I could get these cylinders assembled. Got them back in a week. Woulda got them back sooner if I had put my phone number in the box.

Still, appreciated the quick turnaround. Paul did tell me he had to make a couple special tools to do them cause he didn't realize how small the S3 bore is. I'd say he can do S3 cylinders no problem now.
Anyways, finished up holing up the piston I sent him and start throwing this thing together. Cylinders came out excellent for one minor flaw.The jug is a half mill too far.
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Carb is up better but I shoul;d have scalped another mill off. I had to grind the plug alot anyways but this did make the fit better.
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I was sitting here one day after talking to Moo a bit and was trying to figure out how I added this up wrong. I had taken a bunch of measurements, was pretty sure what I told Paul to take off, how'd this come out light? Somehow when I was drawing this up, guess I got confused, combined two numbers or something, and came up with the wrong amount. Sad thing is......If I had been reading my notes in my phone, instead of using scribbled numbers on paper, the last pic would have been avoided.
One thing I did learn is that with the cylinder scalped a tad light, I'd likely had to raise the exhaust port to lower the compression anyways, this will give me a chance at spacing the cylinder around to see what makes the best power. The head gasket was giving me a half mill clearance back along and with the head recess, it still was just too tight. I grabbed the stock gasket and it's pretty paper thin. I had some thicker material so I cut new base gaskets and put them on. The material was thick enough to get the piston below the deck so between all that, crushed down left me with me at .035 clearance. I talked to John a bit and decided to button it up and try it out.
It's a little dirty but I figure I'm gonna have it apart a couple times before finishing it. You can't even see the intake in the first pic. Blends right in.
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Not bad looking I think. The air box is last after I get the jetting real close. Couple growing pains with it like the petcock hitting the carb, cables not long enough, choke tops not fitting the new carbs, ect, I got past most of that. Today I got it buttoned up enough to start it. After kicking it for some time it wouldnt start. Carbs just weren't feeding fuel. I dumped a little in the carbs, gave it a few kicks and it came to life.

Below is a small vid. I revved it on and off up to 4500, nothing hard right yet, motor runs like a swiss clock. One thing I did note though is these old TNT's must have had the baffles knocked through. They sound like stingers and they are loud. I rode it around a little (its raining here) but it was obvious it was a totally different engine. It's running lean so some jetting is in order but when I did get it revved up around 4500 and it came on the pipe, even with a 15 on the front, it lurched hard launching the bike. You can definitely tell there's more power here. The jetting is close, idles well but I think i need to look at a couple larger mains and different needles. It faded quick when i'd try putting my foot in it. I got a day off this week so I'll take time to get it right when it's warm and sunny.
http://youtu.be/Bvna2juzXWU