There is no possible way to see why your car is doing that....all anybody can do is guess. And it could very well be wrong. Truthfully it could be any number of things. Anything can make an engine run less efficiently than it did before.
My simple guess, considering your car is stock.
When you get above 3-4k RPM...when you switch gears, your turbo is surging. All MSP's do this stock...because the engineers went major cheapo.
That alone is not the only problem.
Could be a leaking turbo, could be bad plugs, could be bad gas.
You just have to know how an engine works and take the time to make it run better.
I would invest in a digital tuner and go from there.