This seems to be one of those "98" things.. Your ECM not communicating with autozones scanner could be a different problem....or...autozone's scanner.
Could be the crankshaft sensor, but there is a service bulletin below that was released to correct this issue:
You might need this update done to your ECM:
PCM - No Engine Restart/Rough Idle After Hot Soak
NO: 18-09-98 Rev. B
GROUP: Vehicle Performance
DATE: Jun. 12, 1998
No Restart/Rough Idle
After A Hot Soak
THIS BULLETIN SUPERSEDES TECHNICAL SERVICE BULLETIN 18-09-98 REV. A, DATED MAR. 13, 1998, WHICH SHOULD BE REMOVED FROM YOUR FILES. ALL REVISIONS ARE HIGHLIGHTED WITH **ASTERISKS** AND INCLUDES NEW SOFTWARE FOR ALL APPLICATIONS, THE ADDITION OF THE 3.5L ENGINE, AND ADDED PROCEDURES FOR THE 2.7L ENGINE.
1998 (LH) Concorde/Intrepid
**1999 (LH) LHS/300M**
**NOTE :THE SOFTWARE CHANGE APPLIES TO ALL VEHICLES BUILT PRIOR TO MAY 12, 1998 (MDH 0504XX) AND THE 2.7L THERMOSTAT MODIFICATION APPLIES TO ENGINES WITH BUILD CODES PRIOR TO 04120198 (THE ENGINE BUILD DATE IS LOCATED ON A LABEL ATTACHED TO THE LEFT REAR VALVE COVER). IN-PLANT MODIFIED THERMOSTATS MAY HAVE A WHITE PAINT DOT ON THE THERMOSTAT HOUSING.**
Some vehicles may exhibit a hot engine no start, hot engine restart with a rough idle, or hot engine restart/die-out. Some vehicles may also exhibit misfire DTC's. This condition occurs after a 10 to 20 minute hot soak and may be aggravated by alcohol blended fuels. Some vehicles may not restart until the engine cools. Fuel vapor build up in the fuel rail may be the cause for these conditions.
Using the Diagnostic Scan Tool (DRB III(R)) with the appropriate Diagnostic Procedures Manual, verify all engine/transmission systems are functioning as designed. If Diagnostic Trouble Codes (DTC's) are present, record them on the repair order and repair as necessary before proceeding further with this bulletin. Cold soak the vehicle outdoors or in the shop for a minimum of 8 hours. Connect a fuel pressure gauge Miller Tool C4799 to the service port for the 3.2L or **3.5L** engine. On 2.7L engines, use Miller Tool C4799 plus adapter 6539. Perform fuel bleed procedures on the 2.7L and disconnect the quick connect fuel line at the rear of the engine, just below the throttle body (Figure 1). Connect the adapter 6539 to the fuel line and the pressure gauge C4799 to the adapter.
Switch the ignition key to the "run" position while monitoring fuel pressure. Do not start the vehicle. Allow the fuel pressure to stabilize (approximately 48 to 50 psi) and switch the ignition key to "off". Monitor the fuel pressure gauge for 15 minutes. If the fuel pressure drops 20 PSI or more, the fuel pump module will require replacement along with the flash update Repair Procedure. If the fuel pressure drops less than 20 PSI, perform the flash update Repair Procedure only. **Additionally, If the vehicle has a 2.7L engine perform the thermostat modification and heater hose modification Repair Procedures. **
NOTE :WHENEVER A POWERTRAIN CONTROL MODULE (PCM) IS REPLACED DUE TO FAILURE, THE SOFTWARE OF THE REPLACEMENT CONTROLLER SHOULD BE VERIFIED FOR THE LATEST REVISION LEVEL. USE THE FLASH PROCEDURE TO UPDATE REPLACED CONTROLLERS AS NECESSARY.
NOTE :THE MDS AND DRB III ARE REQUIRED TO PERFORM THIS REPAIR AND THE SYSTEM MUST BE OPERATING WITH RELEASE 21 OR HIGHER AND TIL CD RELEASE **1161** OR HIGHER MUST BE INSTALLED.
POLICY: Reimbursable within the provisions of the warranty.
Labor Operation No: 08-19-40-97 Reprogram, PCM 0.5 Hrs.
14-50-01-90 Module, Fuel Pump Replace 0.8 Hrs.
07A0-01-91 Thermostat, Modify 2.7L 1.6 Hrs.
24-46-10-96 Heater Hose, Modify 2.7L 0.5 Hrs.
FAILURE CODE: FM - Flash Module XX - Service Adjustment