I would lose the pipe. They make 'tuned pipes' for engines which are supposed to increase performance at a given throttle setting, and they are adjusted specifically for each individual engine. When you first put on one you are far from max performance, even running below optimal rpm range.

Point is that a long tube like you've got can really affect how the engine runs, and can definitely cause it to run worse than it was before.

I would lose the pipe, at least until you get your problems fixed. If then you decide to put it back on, you can figure out if it was a factor or not. I think it will probably do more harm than good.