Several thins COULD be going on here...
1. If you did seize the engine the first time you ran it out of gas (unlikely that an engine will seize just from being out of gas) it is possible that the piston ring got welded to the cylinder wall. Upon trying to jump it later you can break the ring lose and the engine will run (not very well but it will run).
2. The "crap" from the gas tank (or water, or a build up of gum if the bike has been sitting for a while, etc) could have F*ed your carb. Turn the petcock from the gas tank off and remove the float bowl (at the bottom of the carb there is a bowl with a big nut under it). Take this nut off, there will be gas in the bowl so have a bucket handy and put something on the ground to catch what you spill. Look at the gas in the bowl to see if there's any water in the gas or if there's any gunk in there. If there is you will need to either clean the carb yourself or have someone else do it.
You are premixing the oil and gas correctly right? If not the engine may have already (or will soon) seize.
I would check the carb first and then pull the head to look at the top of the piston and the rings. If they look clean (not pitted or blackened and the rings look okay) then I wouldn't bother pulling the cylinder. If the piston looks pitted, or the cylinder wall if scored then you're gonna need to rebuild it.
If you want tips on rebuilding just shoot me an email (pmoravec at blast dot net)
--Paul
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