Pop off is your needle and seat. The needle and seat is closed at idle. The spring holds it closed. As soon as you get off idle, the increased pressures compress the spring, allow the needle to open and deliver fuel to the system. Too low of a pop-off and the vibration in your motor will cause the needle and seat to leak, allowing too much fuel in and the system will run rich. The motor will load and bog, and have no performance. If the pop off is too high, the fuel will be delivered late, and the ski will lean stall. Generally speaking, you want to have the lowest pop off pressure you can have to have the best throttle response.
Someone please correct that if it is not correct.
I do not know what your pop off is or what it should be. The only way to know is use a tester. Even the same needle, seat and spring on 2 different carbs could give 2 different pop off readings. You have to use a tester on your system to find out what it is for sure. I'm not very good at tuning carbs, but it's not likely you have a pop off issue.
You always need to tune your carb for your ski. Even if you take it off one 650 and put it on another, you have to dial it in for your motor. You changed motors completely, so tuning will be necessary. I don't know which way, follow the advice the others posted. They know more.
There's 2 important things you should walk away with after reading my post.
1) tune your carbs, start rich and don't get lean, check your plugs and listen/feel your throttle. They will tell you what is wrong.
2) Don't assume the thing you know the least about is the problem. You have asked 3 times if your pop off is the problem. Start with what you know and work from there. You know main, you know pilot. Get them right first, and you'll probably find out that you don't know about those other things because they aren't very often the problem.
Lastly, as a side note, you did mod your pipe. if you messed it up, it could make for some tuning problems. From what i read about moding the stock 650 pipe, it's a pretty straight forward job. Nothing too crazy, so that is unlikely your problem.