When you say "new top end" do you mean the piston ?? , or do you mean the piston and the valves were replaced as well ??
If the valves had been just adjusted , that means they are moving , once they start moving (in need of adjustment) then they will continue to move till there is no adjustment left due to shim size limitations , sometimes it is 20 or more hours in between adjustments needed , sometimes it is only a hour or so depending at which stage of wear they are .... basically the valve face wears , and as it wears the gap from the stem to the cam closes up , the shims take care of that space , once you get to the smallest shim , there is no adjustment left and the valves zero out , which means they will eventually hang open slightly , it can even get to the point where the valve face gets so thin , it snaps off and then you have a major issue with the valve head breaking off and going thru the piston or cylinder wall .... so those things need to be verified .... also (depending on who did the work) was the Timing Chain replaced ?? , has the timing been checked ??
Does it pop/backfire thru the muffler when you let off the gas while riding ???
What is your Main Jet size ?? , and what is your elevation ?? , did you check the adjustment of the Fuel Screw ?? , it should be around 1-7/8 turns out from lightly seated , then go from there in/out to get the highest idle ...
Here is the Jetting Specs , check your elevation and make sure yours is adjusted and set up like the chart
I am guessing you have had the carb off , if so how was the Hot Start working ?? , if the Hot Start plunger is stuck it can cause issues , the lever should work freely and snap back when used ...
Also , is it real easy to kick over or really hard (to push on the kickstarter) , as it could be possible the Decompressor is stuck , that might make it harder to kickstart , but it would push start fine .... Has anyone done a Compression or Leak Down Test on it ??
If you are sure it is jetted correctly , then my first guess would be valves are out of adjustment
If you have some mechanical skills , I can post pictures from the Service Manual to guide you thru checking the timing , valve adjustment , etc. ...