Backfiring into the intake manifold only occurs when there is either a lean mixture, sticky valve or crossed spark plug wires.
Do all the testing on a warm/hot engine since that is when your problems occur. Start at the top of this list and work your way down. Do all the steps, and don't skip any. Avoid throwing parts at the problem in place of careful test and evaluation.
1.) To eliminate the easy stuff first, check the firing order. Since you are not the car's original owner, check to verify that it is indeed an HO engine. Remove the #1 & #3 spark plugs. Put your finger in #1 spark plug hole. Crank the engine over until you feel compression on #1 cylinder. Slowly turn the engine until the TDC mark and the timing pointer line up. Mark TDC on the balancer with chalk or paint. Put your finger in #3 spark plug hole and crank the engine 90 degrees. You should feel pressure trying to blow past your finger. If you do not feel pressure, repeat the process again. If you feel pressure, it is a HO engine.
No pressure the second time, remove spark plug #5. Put your finger in #1 spark plug hole. Crank the engine over until you feel compression on #1 cylinder. Put your finger in #5 spark plug hole and crank the engine 90 degrees. If you feel pressure now, the engine is not a HO model, no matter what it says on the engine.
Using a small carpenter or machinist square to mark the harmonic balancer off into 90 degree sections may be helpful here.
A 15/16 deep socket & breaker bar or ratchet may be used to turn the engine.
The HO firing order is 1-3-7-2-6-5-4-8.
Non HO firing order is 1-5-4-2-6-3-7-8
2.) Check the plug wires, distributor cap and rotor for carbon tracks or evidence of spark jumping around. The spark plug wires are best checked in the dark with the engine running. Look for sparks jumping or a blue glow around the plug wires
3.) Buy or borrow a vacuum gauge. You should pull 18"-21" of vacuum at 1000 RPM. The vacuum gauge needle should be steady, it may vibrate a little. If you see large sweeps of the vacuum, more than 2" change, or low vacuum - 8"-13" you have a vacuum leak or a sticking valve.
4.) Do a cylinder balance test to eliminate weak cylinders or bad injectors. Warm the car's engine up to normal operating temperature. Use a jumper wire or paper clip to put the computer into test mode. Start the engine and let it go through the normal diagnostic tests, then quickly press the throttle to the floor. The engine RPM should exceed 2500 RPM's for a brief second. The engine RPM's will increase to about 1450-1600 RPM and hold steady. The engine will shut off power to each injector, one at a time. When it has sequenced through all 8 injectors, it will flash 99 for everything OK, or the number of the failing cylinder such as 22 for cylinder #2. Quickly pressing the throttle again up to 2500 RPM’s will cause the test to re-run with smaller qualifying figures. Do it a third time, and if the same cylinder shows up, the cylinder is weak and isn’t putting out power like it should. See the Chilton’s Shop manual for the complete test procedure
Here's the link to dump the computer codes with only a jumper wire or paper clip and the check engine light, or test light or voltmeter. I’ve used it for years, and it works great.
See
http://www.troublecodes.net/Ford/
OR
See
http://www.dalidesign.com/hbook/eectest.html for more descriptive help
OR
See
http://www.mustangworks.com/articles/electronics/eec-iv_codes.html
For those who are intimidated by all the wires & connections, see
http://www.actron.com/product_detail.php?pid=16153 for what a typical hand scanner looks like. Normal retail price is about $30 or so at Walmart.
Or for a nicer scanner see
http://www.midwayautosupply.com/detailedproductdescription.asp?3829 – It has a 3 digit LCD display so that you don’t have to count flashes or beeps.. Cost is $33.
5.) Get a good analog voltmeter or a DVM with an analog bar display to check the TPS. Use the green and black wires to take the measurements. At idle you should see less than .99 volt, at WOT you should see more than 4.25 volts. Open and close the throttle slowly several times. You should see a smooth and steady change as you open and close the throttle. Any jumping around means that the TPS is defective.