Tune up-ignition questions

If it starts and runs then the coil is hooked up correctly even if it idles rough. Now you can not go by the notch on the cap to set the firing order. Remove the #1 spark plug and bump the starter until it is on top dead center, you will here air coming from the hole(compression stroke). Now remove the dist cap and look and see where the rotor is pointing and the tower in the cap that matches that position this is where you want to start the firing order from and go clockwise from that point. Check the reference section and there are engine manuals that will list the correct firing order for your make/size engine, you didn't say what engine you have I would assume its a ford 351W but assuming makes an ass out of you and me both, so look in the reference section of this web site and you will find all of the specs for your specific engine.