Idle Problems (please Help)

You have changed the heads and intake manifold on a car the originally had a Speed Density computer system in it. If you still have the Speed Density computer and not a Mass Air computer system like on the 89 and later 5.0 Mustangs, that is the source of your problem.

Speed Density uses Manifold vacuum (MAP), Throttle position (TPS) and RPM, Air Temperature (ACT) & Engine Coolant (ECT) to guess how much air the engine is pulling in. Then it uses all of them to calculate the air/fuel mixture. It is dependent on steady manifold vacuum and minimal changes in airflow from the stock engine configuration to maintain the proper air/fuel ratio. Change the airflow or vacuum too much and the computer can't compensate for the changes, and does not run well. Forget about putting a supercharger, turbocharger or monster stroker crank in a Speed Density engine, because the stock computer tune won’t handle it. Every time you seriously change the airflow through the engine, you need a new custom burned chip to make the engine run at peak performance.

Mass Air uses a Mass Air Flow meter (MAF) to actually measure how much air is being pulled in and uses the inputs from the TPS, ACT, ECT, RPM and Barometric Pressure sensor (Baro) to calculate the proper air/fuel ratio. It is very tolerant of changes in airflow, and vacuum and tolerates wild cams, high flowing heads, and changes in displacement with minimal difficulties. Larger injectors can be used with an aftermarket calibrated MAF or a custom dyno tune. This makes it possible to use the stock computer with engine displacements from 302-408 cu in, and make many modifications without a custom dyno tune chip. Put a new intake manifold on your 331 stroker and the computer figures out how much more fuel to deliver without having to have a new chip burned to accommodate the extra airflow.

MASS air conversion instructions from http://www.stangnet.com/tech/maf/massairconversion.html FREE
A9L (5 Speed) computer from junkyard $100-$150
A9P (Auto or in a pinch, it will work in a 5 Speed car) computer from junkyard $100-$150
70MM MAF from 94-95 Mustang GT - $40-$70
MASS Air wiring harness kit $30-$85

The whole thing is probably less than $300 using junkyard parts.

A9L computers are 5 speed only
A9P computers are automatic, but will work with a 5 speed.

The conversion harness seems to work well for most folks. It avoids the compatibility problems in using a harness from the junkyard. Simple and cheap, actually less work that swapping the wiring harness.
Conversion Harness kits & parts
http://www.mass-air.com/
http://oldfuelinjection.com/index.php?p=54

If the idea of moving & soldering wires scares you, here's a list of compatible Mass Air wiring harnesses.

Copied from bbunt302
Just for reference, here's a list of all the compatible years:

89 harness should work for 86-89 as long as you're using mass air.
90 harness will only work in a 90. (B/c of air bags and dual dash connectors)
91 through early 92 harnesses should be compatible (single dash connector, fuel pump relay under driver's seat)
Late 92 through 93 harnesses should be compatible (single dash connector, fuel pump relay under the hood)

Larger MAF to go with Mass Air conversion:
94-95 Mustang GT MAF - $40-$100. It is 70 MM instead of the stock 55 MM on regular stangs built prior to 94. It uses a slip on duct on the side that goes to the throttle body and a 4 bolt flange on the other. You need a flange adapter to fit the stock slip on air ducting that goes to the air box. Wiring plugs right in with no changes. *1 *2

*1.) Metal flange adapter http://www.kustomz.com/cat3.html Buy the TR70 for $40-$45 depending on if it’s on sale or not. Or spend some time on eBay looking for one that may fit.
Try AutoZone and ask for 81413 - Spectre / 3 in. Aluminum Intake Mass Air Flow Sensor Adapter at $12.00. You may have to order it online.

*2.) MAF & sensor interchange
The 94-95 Mustang 5.0 MAF & sensor is also found on:
1995-94 Mustang 3.8L F2VF-12B579-A2A,
1994-92 Crown Victoria 4.6L F2VF-12B579-A2A,
1995-94 Mustang, Mustang Cobra 5.0L F2VF-12B579-A2A,
1994-92 Town Car 4.6L F2VF-12B579-A2A,
1994-92 Grand Marquis 4.6L F2VF-12B579-A2A,
Evidently the –A1A, -A2A, AA, etc. on the end of the part number is a minor variant that did not change the operating specs. You should be able to ignore it and have everything work good.