1) Firing order for your car is 13726548.
2) Your 5.0's distributor turns counterclockwise.
3) The #s on the cylinders read like this: standing in front of the car facing the engine, on passenger side of vehicle starting at left side, closest to you (farthest from firewall) is # 1, then going back toward the firewall is #2, then #3, #4. Then starting on right side (driver's side) closest to you is 5, then going back toward firewall, #6, #7, #8.
So with this information you can make sure you have the correct arrangement of plugs (firing order).
For example, looking at the distributor cap, you can see a "1" on the top. Starting from "1" on the cap, circle like a clock, but counterclockwise and the next is 2 (not read), then all the way to 8 notches. Match them up to the motor in the correct way using the info above.
As far as a shorter plug wire. Just about everytime I've gone to get new plugs for my Mustangs (whether the '92 or the '79, the coil wire in the box is wrong (too short), but the rest are right, and many times I've just left the old coil wire on there....
Also, make sure you check that you didn't knock off any vacuum hoses (coming from your intake or anywhere else) or that none of your hoses are corroded or old and weak b/c a rough idle is sometime indicative of bad vacuum, but REALLY rough idle in your case is more likely messed up fireing order, but you may only have 2 crossed if any, b/c if it were more than that, the car would barely run right, which doesn't seem like your situation.