If you're thinking about doing the HO conversion later on and have parts accumulated, you may be tempted to throw them on now. Or if you don't want to do the full HO conversion but would like a little more power, you might be looking for a way to do that. This section is designed for you.
You must first realize that the very heart of the HO motor vs. your stock 5.0 is the camshaft. Without the HO cam, you don't have an HO motor. Although the HO cam runs short on upper-RPM power, it's still miles above our stock cam. However, the HO cam requires a lot of other components and things to make it work correctly: the computer, firing order, larger fuel injectors, and MAP sensor. This being said, there are things you can do to make more power out of your stock 5.0 without changing all those things. A few of them are listed below, and all are parts that you would need for the full HO conversion anyway. The horsepower estimate, after all components below are installed, would be in the neighborhood of 190-200hp.
The stock 1986-88 Cougar heads are, to say the least, very restrictive. Narrow inlets and "high swirl" exhaust ports add to fuel economy, but at the expense of good power. These heads were also used on the '86-'88 Thunderbird, the '86-'91 Crown Victoria/Grand Marquis, and the '86 Mustang GT. In '87, the Mustang received the F-150 truck heads (a.k.a. the E7TE-AA castings); the Cougars still had the restrictive heads through 1988. This is the most obvious point to start. You will gain approximately 15hp over the stock heads and experience much better upper-rpm power. You can drop these heads on anytime you wish. With the stock E7TE heads, you will reuse your pushrods and rocker arms. GT-40 heads and Trick Flow heads, among many others, can also be used, according to your budget. Also, should you wish to port and polish your new heads, or install stock-ratio 1.6 roller rockers, you can do that with no ill effects from the standard output camshaft.
There is a minor difference in casting between the non-HO and HO plenums, the difference being a larger inlet for a few more horsepower. The stock Mustang upper has the letters "HO" stamped under the removable top plate. If you decide to go with this intake, you should install the matching EGR plate and EGR valve from the Mustang as well; this will give you maximum airflow performance. By the way, the non-HO and HO lower intake manifolds are all the same. If you are thinking about getting your intakes Extrude-Honed, the Mustang HO upper is an excellent (and stealthy) choice, flowing nearly as well as a GT-40 intake after honing.
Another option is an aftermarket upper and lower intake combo. Your choices are limitless now: Cobra, GT-40, Edelbrock, Trick Flow, Holley, etc. It all depends upon your budget, but keep in mind that your engine is a fancy air pump. Too much airflow with the stock speed density computer may bog down the motor upon acceleration. Also, a heat (phenolic) spacer is a popular item and is worth looking into if you're so inclined.
The stock Cougar/Thunderbird throttle body is a rather restrictive 50mm. The stock Mustang throttle body is better at 60mm. Your stock one will work if you can't get the bigger one, but your car may hesitate slightly upon acceleration due to restricted airflow.
If you're shopping new, a 65mm aftermarket unit will still work with the stock speed density computer and give you much improved airflow. Anything over a 65mm throttle body on a stock motor will decrease low-end torque and actually bog down the motor with too much air. These bigger units should be limited to severely modified motors only. Also, be sure to buy a throttle body made for 1987-up Mustangs—the 1986 throttle bodies were unique. And remember to get a throttle position sensor (TPS) to match the new throttle body, as your stock one may not work.