OK, so let's get the information straight so someone can help you for real.
1) The engine was in an unknown running state
2) you didn't check compression before the full or partial disassembly.
3) the ground up rebuild, is not a rebuild at all.
4) you took the cam out, and or removed the timing chain at some point (i'm confused on this point) and put it back in, but can't remember if you lined up the dots?
5) you never checked static ignition timing before attempting to start the bike
6) you're running race carbs on a street bike with no internal mods whatsoever
would you say this is pretty much accurate?
1) I did see the engine run before buying the bike. The guy that sold it to me pulled off one of the carbs, shot a little starter fluid in it, and it started right up. I should point out that I bought it for $350 so start is about all it did.
2)You are correct. I did not compression test the bike before pulling the top of it apart. I assumed because it started and ran it was ok in that department?
3)Your right, I removed the engine, took the frame to bare metal and modified it, replaced or upgraded all of the non-engine parts I could, but I guess since I didn't completely rebuild the engine it's not a "ground up" rebuild.
4) Some of the fins were broken so I replaced the cylinder head and redid the valves. I did not do the rings. I followed the step by step procedure for this in the Honda manual and cross referenced this site when I needed help. The outcome was good, or so I thought based on compression testing.
5) Simply put... No. Does the Dynatek S require that?
6) Again, Simply put. Yes. The only modifications I have made are the Dyna coils, the Dyna S kit, Carpy's Yoshi knockoff 4-1 exhaust.
Any help would be appreciated. Thanks in advance.