Re: aftermarket brake lines...
yes, the new lines should of came with a longer banjo bolt that goes into the master cylinder.
in theory, having two separate lines going straight from the source applies equal pressure to the two brake calipers instead of the right caliper getting the most force and having the excess pressure bleed over to the left caliper.
its one of the benifits to getting aftermarket lines in addition to less flex in the hose.
make sure you bleed them well and put a good fluid in there, especially since you are riding on the track.