Larger PJ38 Choke Problem

[CR500PHIL]

I previously started a thread about a PJ38 choke problem well now there is definitely more to the problem than first thought so I decided to start another thread. Here is the problem: the problem is more than just a the choke rod. I was sent another by the guy I bought the PJ38 carb from and it is in mint shape. I also cleaned the entire carb. I put fresh gas in the bike too. I start the bike and it requires more kicks than it should. Once running the bike runs perfect and once going starts first kick afterwards. The strange thing is applying the choke has no effect while the engine is running - does not increase RPMs or anything. Since the choke is the idle adjustment, the idle adjustment has no effect either. Basically it seems I am starting the running without a choke even though I apply it. FYI I am running the bike without an airbox / filter now since I still have the bike on the jack in my garage - could this have an effect? Also is it possible that the fuel height is too low for the fuel to "reach" the starter jet? This is very strange.