Would not having an exhaust on with the emissions removed be bad for the apex seals? I was told by someone that without backpressure it really messes them up. I had the part that comes off the turbo but instead of where the first flange is there is one of those cheapo mufflers on it.

 

I'm not exactly sure what you're saying, but it won't hurt the engine to have a more open exhaust. What can happen if you have an open exhaust with the stock wastegate, is that you can cause the car to overboost, create a lean condition and blow the engine. Are you saying that you have a muffler in place of where your downpipe should be?

 

Well right were the part thta bolts to the cat the flange is cut off and a cheapo muffler from autozone is clamped on it. Altogether the exhaust is about 2 to 3 feet long.

 

That and a short intake run is how you move the power band up.
Of course it falls flat without a port job to let it breathe.

As Snrub said, watch out for boost creep..