When you say wont work,what do you mean. Does it click and not turn,it does nothing,what? you need to be more specific!
Battery needs to be fully charged ie 14 volts or better not 12
Are the interior lights/accesorys getting power?
Headlights?
did you reconnect the start terminal on the factory solonoid on the fender?
Are your cables in good shape and of good quality? Standard auto store replacement cables suck, they usually are to small a gauge and then they cover them with thicker covers to make them look bigger. I use only Delco or genuine Ford.
You should have a negative cable from you - battery to the block or timing cover,a 10 gauge wire from you - battery to a clean(no paint) body mount, there should be a ground strap from one of the heads to the firewall,all are important.
With the FMS starter you will have a cable from positive battery terminal or the primary terminal on the fender solonoid to the post on the solonoid on the starter. Then you will have a 10 or 12 gauge wire from the secondary side of the fender solonoid to the spade terminal on the FMS starter. If you are running your + battery cable directly to the starter, you must still supply 12 volts to the primary side of the fender solonoid.
With the factory starter the + cable goes to the fender solonoid(primary) and then a second cable runs from the secondary side down to the starter.
Again remember to reattach you trigger wire(it runs from your ignition switch to the fender solonoid) or nothing is gonna happen