It sounds like what has happened is that the prawl on your stock clutch quadrant has broken or teeth have broken off of your quadrant.
These items are barely adequate for even the stock clutch. When you install a clutch with a heavier pressure plate (like a stage 2 anything), these parts break.
The fix is to replace these items with aftermarket pieces and to install a Firewall Adjuster along with a new OEM style cable.
Take a look at
http://www.maximummotorsports.com/Clutch-Cable-Quadrant-and-Firewall-Adjuster-Package-P385.aspx
This kit has everything you need to replace those pieces and will hold up to just about any clutch you can think to install. This is the kit that I installed (many moons ago). Had I to do it over again, I would have gone with the Fiore Micro-Click firewall adjuster. Fiore is now out of business but there's a company out there that has the rights to make them (I don't recall who it is but someone else on this forum should know and be able to tell you).
When you lay on the driver side floor looking up, you will see the whole assembly. Here's a pic of that assembly so that you can get your bearings if you're not familiar with the setup:
Edit:
One other possibility is that your clutch fork is not seated in the correct position. Check the quadrant and prawl first though.
Do not under any circumstances, install a cable that is not Ford OEM quality. There are two sources for such a cable that I'm aware of... Ford and Maximum Motorsports.