I have put back my stock end cap and now the DS is bogging when throttle is almost full on 1st-2nd gear and fuel is coming to the air box. I realy don't know what happened because I haven't changed anything when moded the end-cap.
The drain screw at the bottom of my stock carb is all the way closed, when I open it, fuel is flowing from the drain hose.

Could someone tell me what is the problem and if the drain screw should be closed?

 

Drain screw should be closed.

If the bike was jetted for a aftermarket end cap and you replaced it with a stock end cap then you are more then likely running too rich.

 

Yes, exactly what that dirty rotten Scoundrel said.
If the bowl screw were to stay open at all, fuel would come out all the time. The more it's open, the more fuel wasted. If you get water in the carb it will be the screw you open to get it (the water)out.
As fart as your bogging trouble, 165 jet is stock and best with the stock cap. 175 with the open end cap. That is here in FLORIDUH.

 

If you didnt rejet after opening up the end cap maybe you got a float problem, also check to make sure your choke is all the way off. there are to positions on the choke make sure, its pushed all the way in. I have had it happen to me. just my .02

 

I also have pops comming from the air box, should I try to adjust the idle screw? can it solve the bogging problem?
Please help [img]i/expressions/face-icon-small-blush.gif[/img]

 

You may also consider having your valve clearances measured and adjusted if needed.