iketheband,
Do you have a power booster on your master cyl. setup? That might make a difference, but you are likely looking at some required rerouting of the brakelines to clear the shifter linkage. I hope to reroute mine this weekend and I can post here to let you know how it goes. The booster could shift the entire master back farther which would allow the brake lines to clear the transmission linkage. You would have to look at the position of the master relative to the transmission and see how close they come.
Hope this helps.