clean you air filter, clean your IAT and MAF (they get dirty due to the oil filter) i also suggest cleaning out the intake pipe, as the PCV can allow oil into it. Clean the throttle body in FRONT of the butterfly flap. behind the flap has a ford specific coating to prevent build up.
I also suggest chaing all the fluids, as mentioned above. your coolant system is probably full to the brim with yuckies. lol. use distilled water when making your 50/50 mix.
other than the rest of your fluids, you should balance and rotate your tires. check your tires and match the PSI to Ford's specs.
serpentine belt (previously mentioned) is a good idea, and as long as you have it off, you might want to think about doing the tensioner. This isnt mandatory.
check your suspension. Inspect all bushings for total-decomposition. this includes your motor mounts.
Inspect your brake pads. if they seem low, replace them.
check your rotors. if they have cracks (major cracks) replace them. if they have hairline cracks, monitor them closely, as these can VERY quickly grow and become problematic.
while chaning your tranny fluid, inspect the small plastic cup the shifter sits in. if this cracks or breaks, you will not only have debris in your tranny, but it wont function properly.
replace your PCV valve. Although many feel this isnt mandatory, for $2.99... you might as well.
inspect and replace your o2 sensors as required.
take off your Transmission's dust shield and inspect your shift fork. try and gently jiggle it. if it makes sounds, you may have a bearing going out. Dont jerk on the fork, as you may dislodge it somehow.
take off your harmonic balancer. inspect it for cracks, wear, and tear.
replace your front main seal when you do this. Felpro front seal is $10.00 and a 30 minute job.
inspect your sway bars (front and rear) for cracks. These are hollow and have been known to fail.
grab your driveshaft and jerk on it a little... if it rattles or moves, this could be a sign of your U-joints going out.
inspect the gasket on your gas-tank fill tube. These go out after about 10 years. if you see any signs of fluid around teh base of the fill tube, replace teh gasket.
inspect your coolant over flow tank for leaks. after about 10 years, these can go bad.
if your coolant exansion tank cap looks "popped" out at all, replace it. its is going to fail soon.
inspect your gas cap for cracks or breaks, a faulty gas cap can cause codes to be thrown, increase vehicle emmisions, and make your car smell funny. I suggest a locking cap if yours is broken.
inspect all lightbulbs around your vehicle. these are interlaced into the wiring system of the car and a bad-bulb can cause other problems. a perfect example is a bad brake light bulb causing your cruise control not to work.
clean your battery terminals with baking soda and water to remove corrosion. replace the felt washers, apply protrolium jelly to the terminals and reconnect the battery.
inspect your radiator's passenger side wall for hairline cracks. this is where the radiators on the modular mustangs fail most often.
inspect your ball joints. take off your front wheels and measure the ball joints. if one is higher up than the other, replace them both immediately. do not drive your car.
if the hight is roughly the same, grab on to each one and wiggle it around a little. listen for odd sounds (metal on metal) and check for ease-of-mobility. Our ball joints are not servicable, and when they go out it can be detramental.
inspect your header bolts. ensure that all of them are still in and tight.
inspect your motor mount bolts. ensure they are all in and tight.
thats about all i can think of now... i chose not to mention changing oil or fuel filter because that was already mentioned.