It might be a problem with the electric choke coming on when its not supposed to but your earlier posts make it sound like it was too lean.....When it starts to die I would just hold the throttle down and let it quit...Then pull the spark plug and see if its is wet or dry..This should tell you if its getting too much fuel(choke) or not enough(fuel delivery problem).Do you have an inline fuel filter?..If so make sure it is clean..IF you don't you should get one in case there is dirt coming from the tank...I'm not surprised it didn't run well in 40 degree temps with the air cleaner removed as both of those conditions will lean out the air fuel mixture...Your needle is normally in the middle position..You could try raising it up or down and see what effect it has..Raising the needle one notch made a nice improvement in acceleration on our viper...

 

sounds like you did not bypass the gas tank.. now remove the shutoff valve and clean the screen at the end of the valve in the tank...collect the fuel in clean container

 

I am having the exact same issue with my daughters Scrambler 50. Half the problem seams that the clamp that clamps the carb to the intake had a stripped screw so it was not getting tight enough to prevent air from being sucked in after the carb. I replaced that with a hose clamp. The same issue shows up everytime I start it and I have to let it idle for about 1-2 minutes for the auto choke to shut off. Then it runs 'decent' but still seems to never kick into the power band.

 

I have been having very similar problems with my 02 scrambler 50. I'm trying to get it ready to sell, but it needs a lot of work. It starts first kick, but then wont idle. If it does idle, i cant push the throttle in more than like you said 1/4 of the way without it bogging out. i removed the air box, and played around with the idle screw, but it seemed to have no affect. I have cleaned the carb numerous times, and it hasn't made a difference. I drained the gas, and put in fresh gas. still no change. sometimes it will run enough that I can ride for a few mins, but if I take a corner or lose speed, it loses power and dies. I'm also having trouble with the spark cap. It doesn't seem to want to stay on the plug. At first i thought this was the problem, but I don't think so. Any advice?

 

Many troubles with the elec choke carbs!
Ask airmobile101. I think he messed with those carbs.