Is it the stock Carter carb or the Weber carb? If it is the Carter, I can relate to your problem. The only time mine didn't want to stall was when I first started up and the choke was on. My carb is not new like yours, but these are some things you might wanna check out or try.
Does the Jeep run better after it has warmed up? If so, check your choke setting.... sound like it is too lean.
Does it still run bad after it's warmed up? Then it might be your idle setting, as atomicmoose mentioned. It might be idling too low when the choke comes off. You'd need to turn the idle screw up until it runs smoothly
If that doesn't do it, then warm up the Jeep and then look down into the carb (with caution and safety glasses). See if there is any fuel dripping down into the throat of the carb. If there is, you might need to enlarge your idle tubes like I had to. They need to be drilled out to 0.032". You can get that size drill bit at a hobby store. Go to this address for the how-to:
Check the idle mixture screws. I screwed mine all the way in, then I backed them out a little at a time until I got the smoothest idle.
When all else fails, use some carb cleaner, couldn't hurt. Hope this helps.