I have a 2004 Mustang Mach1, it sat for a month while getting some repairs and now that i got it backit shifts roughly. Sometimes it goes into gear fine, but sometimes it doesnt go smoothly. Does it have a hydraulic clutch? I had the same problem on my Sonoma and it just needed to have the clucth bled. So i think its the same thing if it has a hydraulic clutch. Can anybody give me some info? I searched online but couldnt find anything.

Pretty sure that's a cable operated clutch.  Not much to go wrong, especially on a new one.  Try lifiting the pedal with your foot, that's how they 'adjust' (take up the slack in the cable).  Other than that I'm not sure.  You didn't just change your trans oil did you?  I put synthetic in mine and it was a big mistake, went back to mineral oil and all was good.  Best of luck.