The pilot jet size increase would not have helped anything at 1/8 throttle as it's bypassed except at idle.  If the dying started when you increased that jet, change it back, retune and go from there.  Actually, I'd say it probably shouldn't have been changed in the first place if it was idling okay before.  That said, if the dying didn't start with that change, I'm leaning toward a float problem as mentioned above.  Please read through the Carb references in the Tech Ref forum to try to familiarize yourself better also.  They'll really help your overall view of the problem.

A change in the pilot jet size one way or the other will mostly be noticed in gas mileage, maybe a bit of backfire and very very  slight in performance.  Might blacken the plug a bit.
But your bike is dieing!  And it smells of gas!
I'd be looking for gas getting in around the jetting system.  That is only through the pethingy vac line or the needle/float.

When you just look at the floats, they are hanging (unless the carb is turned upside down.  You want to adjust their upward stop point.  Gently raise them up with your finger until you feel the needle touch the seat.  At that point the flat bottom of the floats should look about parallel to the top of the float bowl.  I'm not saying even with, but the lines should look roughly parallel.  The manual says 1.1" from bottom of float to the top edge of the float bowl.  This is at their upper most point of travel (gentle).  Or if you do it with the carb upside down they will be at rest.

Hope that helps.

Thanks guys.  I put the old jet back in.  I checked the float level and it looked to me like they close to  the bottom of the bowl.  They also moved freely.  I haven't put the tank back on yet, I wanted to get a new plug first.  I will do that tomorrow and try her out.  Thanks again!!!  I really appreciate your efforts and insight.  I wish I had more to offer technically for the forum but if you need any advice on growing tomatoes...

Probert, I think you might have been neglecting one thing, or maybe I did not understand you correctly, when you wrote "It came stock with a #52.5 pilot jet and I've increased the airflow with the muffler. "
You don't increase airflow with the muffler, you increase airflow with the airfilter.
THINK LIKE THIS: The single cylinder engine is like a bucket. The bucket has a lid (the carb) where we pour in air and water (fuel). The exhaust is a pipe leading the air-fuel mixture out of the engine. The effect is the amount of water-air-mixture that you are able to make pass through the bucket in shortest possible time. Ok, so if you get a more open exhaust, more water will run out IF you put more water in. But if you only pour in more water, not air, there will be a vacuum in the bucket, and the flow will not be the expected.
So, you just can't put on a wider exhaust, and go up a bit in jet-size. You must also increase the flow of air. I think your set-up is ok, IF you replace the stock- airfilter in the airbox with a K&N -filter that fits into the box.
Good luck ! 8)

I want to thank everyone again.  I got her running this weekend.  I put the stock pilot jet (#52.5) back in and readjusted the pilot air screw back to 2.25 turns out along with the idle.  The sluggishness at 1/4 throttle is back but she runs good.  I'm still a little confused as to why it didn't work with the #55 pilot.  The black plug and smell of gas suggest flooding to me but...  I assume if I also replaced the airfilter it may work, but maybe next year.  I just want to ride now.  Thanks again!!!

We've just recently been shown a real easy way to check floay levels. Hhok a tube on the cast tube poking down from the bowl & open the screw. The petCoCk should be on prime.With the tube up by the bowl you can see where the fuel level is in the carb. If you dont have a clear tube, that's okay, just start with the end held high. As you lower it, the fuel will drip out when the end of the hose is low enough.