Ok well I figured out the solution to my problem anyway. What I did was I cut the metal brace off of the piece that holds the shifter. I am talking about the length of pipe that attaches to the tranny but not the one that actually shifts the gears. I cut it off right where the bracket starts that holds the shifter. I then drilled a hole through the tunnel about an inch in front of where the shifter comes through the floor. I also drilled a hole in the bracket that holds the shift lever so that when I dropped a bolt through it would line up. I then put about five 1/8th inch washers to space the bracket out away from the floor so it would be even with the floor.

To sum a few things up what I mainly did was cut off the old metal pipe that was bolted to the tranny near the oil pan and made my own bracket to hold the shift lever in place. What this did for me was it kept my shift linkage from contacting anything and allowed my short shifter to work flawlessly.

This is information for a LS swap in a EF hatch with an integra modified shift linkage.

If anyone will inform me in a PM on how to post pictures I will do a step by step for this one incase anybody may need this in the future.