Continuity in South Park 

In this section, the prase "Jesus states he only has special powers when dead, although in "Super Best Friends" he had the powers flight and master carpentry" is false, because he didn't have the power of flight. Remember how they had to fly on a plane in the episode? I changed it to reflect that.
 Even though Jesus takes stan in a plane, Jesus can indeed fly.  When the super best friends gather to defeat David Blaine, they fly down to meet him DC. 
Don't forget that Jesus has the power of healing, when he arrives in Iraq to heal Santa's legs in "Red Sleigh Down".  
Also, he has the power to turn water into wine, and produce mountains of fish (as long as you're willing to turn around for a second).