
sorry, your question is a little confusing (at least to me). Why do you think there is air in the fuel line? In this post you say the engine is running after changing the lines, but in the next post you seem to indicate you can't get it running. "should I just keep trying to start it?" I'm not clear on if it is now starting or not?
My experience after cleaning/dumping the fuel from the filter or replacing a line has been like Doc says, it takes a few seconds of cranking the engine to get fuel back in the lines and then you should be ok. I have the same ski as you and changed some fuel lines and cleaned the filter a couple weeks ago. I cranked it about 10 seconds and it didn't start so I started to wonder too. I unscrewed the filter bowl and it was full again so I just cranked a few more seconds and it started up fine.
If your filter bowl is not filling up again, my GUESSes would be, you are sucking air at the filter (bad o-ring or cross threaded the bowl), the filter inside the fuel tank may be plugged (but you should have had that problem before you changed the lines), you don't have gas in the fuel tank, or you might have connected fuel lines incorrectly when you replaced them (did you do them one at a time to make sure they didn't get crossed?). Anything beyond that is above my pay grade - sorry.