Cracked Fuel Line?

[Bugjunkie66]

Just got an 06 MCS with 77k miles on it. As a new owner I wanted to do my best to maintain the car as a new owner not knowing its history.
Recently changed the fuel filter and had many struggles as I had never done a Mini before. After running almost all the fuel out, changed the filter and reassembled. Car would not start. Added about two gallons of fuel as recommended by some forum I read and still no go even though fuel was on the filter side of the tank. Pulled the pump and found pump side of the saddle fuel tank was dry. I added more fuel into the pump side while pump was out and car fired up and ran good immediately.
After about 200 miles or so on a full tank, car suddenly loses power, sputters and barely runs at full throttle. Turn off and restart and its like nothing is wrong but only runs a few miles before this happens again.
Is it possible that I cracked or broke the fuel bypass line and the pump side of the tank is running dry by no overflow from filter side to pump side?