2005 Mustang GT 6spd shifting issues

I have a tr-6060 6spd that I installed into my mustang. During normal driving the trans works pretty good, a little notchy at times and can be a bit hard to get into first at times, but thats about it. When I have the car WOT and shifting at 6600 rpm it grinds everytime into second and occasionaly into 3rd. Tranny has mobil 1 full synthetic ATF and I have replaced the fluid once. I have vacuum bleed the clutch system using Ford's procedure. Clutch system has new master cylinder, line, and slave cylinder. Does anyone have any tips? The clutch seems to begin to engage as soon as i start to lift up the pedal off the floor. Has anyone out there shimmed there stock slave cylinder? Or used the aftermarket McCloud unit? Dont really like the ram clutch style. Are they hard to get shimmed properly? Also has anyone heard of a cable conversion kit for are cars, because I would buy one in a heart beat!