Ok, got the lines bent and flared, that's all set. I start to "bench" bleed the brakes on the car and the rod is making a clunking sound now, looks like the rod is too short. I re-used the rod hat was on the last master cylinder. Also noticed that the brake doesn't come in contact with the brake light switch now too.
Edit: you think this will solve my problem?
http://www.speedwaymotors.com/SSBC-U...Kit,50351.html