If it runs good once you get going to me that doesnt sound electrical but who knows. Usually if its electrical from my experience it runs WORSE once under load or once it gets into the power band.
List of banshee essential diagnostic tools.
-leak down tester
-compression tester with the proper tip
First put those jets back in (300) and 27.5 pilot. Toomey needles are superior just an fyi but unlikely your issue. I would get a digital multimeter with ohm setting and test all the electrical components, you cant test the CDI but you can test the coil leads and primaries and the stator (and verify that you have all oem electrical components) Then compression test and then leak down test. I wouldnt trust a "shop" to work on anything. I would also pull the stator cover and verify the pick up coil gap (feeler gauge, .018)