The bike is fixed!!!!
Here is the long version. The cause was a stator or weak valve springs (intake). I honestly believe it was just the stator though.
The bike had paddle tires on it so I could not test drive it after I put the stator in. I just raised the rpm's in nuetral and heard the motor cutting out but I think I was actually hearing the rev limiter. I thought the bike still had the issue so I had the head tested and decided to put new intake springs in it just as a precaution and to say "I covered that base". I got a set of dirt tires on the bike after I did the head and test drove it. It worked great. Issue gone. I then raised the rpm's in nuetral and heard the miss due to the rev limiter which is normal of course.
Earlier in the troubleshooting, I had borrowed a set of dirt tires from a friend and used them to test the ICM (CDI), coil, and various carb changes, cleaned the inlet filter, checked the tank vent, etc. The bike failed the test drive after each one of these changes. I had to return the dirt tires so I took the bike home and put in a stator. I could not test drive it at that point so I thought it was still broken. I tried a different carb and it acted the same in nuetral so I decided to put in new intake valve springs. I should have test drove it after the stator. I think that would have done it.
For anyone reading this with a similar problem in the future, this is what I found to check on the bike. These are things I would check first if you develop a high end miss for no apparant reason other than sitting for a few months;
1. New Spark Plug
2. Check for loose wire on coil
3. Check the ICM with a known good one from a buddies bike (These really don't go bad but it is so easy to check that it is just piece of mind; I have never seen or heard of one of these going bad on this model Honda)
4. Check valve clearances
5. Swap coils from a buddies bike
6. TPS (Throttle position sensor on carb). Swap the whole carb if you can find one. Air jets can get clogged and choke circuits can go bad. Carb inlet filters get clogged and so do tank vents; check these also.
7. Change out the stator. Yes, they do go bad, even on a Honda.
8. Pull the head and have it checked out for valve wear and weak springs.
9. If all that fails then go back to step one because you missed one of these.
I spent way too much time on this bike and I hope this will help anyone in the future. I searched the web for people with similar issues and their problems were resolved with loose coil ground wires, bad stators, bad TPS's, and bad heads.