Once you get it into gear does it stay there or pop out? Can you fully engauge the gears with the engine off? There's no slave cylinders in our cars, they're manual clutches. Unless it's aftermarket hydralic or I'm totally mistaken, but every mustang I've seen and worked on had a manual clutch.
Assuming the car still has stock shifter and trans:
First start by adjusting the clutch quadrant (under the dash above the pedals), if that doesn't work, replace the cable, if that doesn't work, replace the clutch and clutch fork, if that doesn't work, take it to a trans shop and diagnose to be sure and replace or rebuild the trans. In that order.
I've had my fair share of problems shifting after my auto to manual swap, but I hope once my firewall adjuster and double hook quadrant arrive next week I will have finally worked out all the bugs.
If you need to I'm sure you can do a search and find directions on how to adjust the quadrant here in these forums, it's pretty easy, just ackward.