There are 3 steps: do them in order, do all of them, not skip around. If you do you will find and fix your problem.
Step 1.) No code 11 (two flashes when the computer dumps the codes)? A perfectly functioning system will always get a code 11, it is the everything is OK code. The 11 code is computer passed its internal self test.
If you don't get an 11, you have computer or wiring problems.
Please check and repost.
Step 2.) Make sure you have the Neutral Safety Switch connector plugged into the transmission. On a T5 it is a pigtail on the front of the transmission on the driver's side.
3.) You guys with idle/stall problems could save a lot of time chasing your tails if you would go through the
Surging Idle Checklist. Over 50 different people contributed information to it. The
first two posts have all the fixes, and steps through the how to find and fix your idle problems without spending a lot of time and money. I continue to update it as more people post fixes or ask questions. You can post questions to that sticky and have your name and idle problem recognized. The guys with original problems and fixes get their posts added to the main fix.
It's free, I don't get anything for the use of it except knowing I helped a fellow Mustang enthusiast with his car. At last check, it had more than 134,000 hits, which indicates it does help fix idle problems quickly and inexpensively.