I have looked over the forums and have not found a problem that is specifically like mine.  I am having issues where I can hop on the bike and it runs find, then a little while later I hop on it and it runs awful.  By awful I mean the engine dies whenever I come to a stop, then last weekend when it was doing it I would try to restart it and smoke would come out of the pipe.  Keep in mind it is usually warm when it starts acting up.  I know I have an oil leak in the front of the engine and haven't determined if it is the "plug" or the head gasket.  I am wondering if the problems are related or if I might have some bad gas or something wrong with the carb.  Any suggestions?

I think I need a little more info...
By a little while later do you mean later in the day, same ride?
If so, does start acting up when you push the 'choke' in?
(ok you guys don't start, I know it's not a choke but an enrichner)
How do you start it? one or two notches out on the 'choke'?

When it does it, look at the spark plug, wet? black? white?

Any back fires?  When?

Could be as simple as your idle speed setting.
Could be you got a vacuum leak in the hose from the carb to the petcock.
Could be you need to adjust the idle fuel mixture.
Could be you need to rejet.

It seems to happen on the second or third ride of the day.  Also it is about 20 min into the actual ride.  By this time if I used a choke at all to start the bike it  would be all the way in.  I have also had problems with it backfiring since I bought the bike in May.  This usually happens wehn I am slowing or when I turn off the bike.  The problem with it stalling has just started to happen in the past few months.  Keep in mind I usually only ride when it is above 50F.  
I replaced the spark plug in June and it looked gray.
Throughout the last few months I have also made sure to take her out every week or two for a spin just to make sure everything is ok.

Have your replaced the spark plug yet? If not, is it overdue. Max

Put 3 ounces of SeaFoam carb cleaner in a full tank or two of gas and report back. You might be surprised. Also draining the carb bowl is a good thing to do Lots of cr@p does end up in the bottom of the bowl.

Is your idle speed high enough? There's a knurled knob on the side of the carb to adjust it.

I have noticed a need to mess with the idle based on temp more than once. It is so easily done, no tools, after a while it gets easy enough to find it without even looking. ( maybe if thats true, I was messing with it too much)