What makes you think it is a chargepipe issue???
The very first thing you need to do is read the codes. If you do not have any, make sure your JB4 has auto clear turned off and try to replicate the issue. If is is as bad as you say it should throw another code.
From the sounds of it your most likely having one of the following issues.
1 - Spark plug
2 - Coil pack
3 - Vanos solenoid
Any of these can cause the issue you described.
Let us know what you find.