I have a 2001 FXDXT with 54,000 miles on it. The engine diagnostic light just started coming on this morning. While it was on, the engine started running rought (felty like it was missing). From what I have read, it appears to be the crank position sensor. Has anyone else had this issue and was it the CPS? Could it possibly be the ignition module? It would help to have some insight before I buy a CPS and replace it.

 

Check the code.
Here's a PDF "by the book" procedure.

Magnetti Morelli codes.pdf

00-03 HD Codes And Activation Link 2

1. Remove right side saddlebag and side cover if so equipped. Remove protective plug from data link connector. Other models will be under the seat.

2. To activate the diagnostic feature,follow these steps.
a. Create diagnostic test wire or use a female spade clip which will bridge the two terminals perfectly.
b. Install diagnostic test wire/clip across Terminals 1 and 2 on the data link connector, they are marked.
c. Turn Ignition/Light Key Switch to IGNITION and wait approximately 10 seconds (4 seconds lamp ON, 6 seconds lamp OFF) for check engine lamp to start flashing.

3. All trouble codes are sent out as a series of flashes. To retrieve the first digit of the trouble code simply observe the number of times the lamp flashes.
a. The lamp will then flash one or more times to indicate the first digit of the trouble code.
b. The length of time the lamp is illuminated and the length of time in which it is off are each about 0.5 second in duration.

4. The second digit follows:
a. Following the transmission of the first digit, there is a 1.2 second pause in which the lamp is off.
b. The lamp will then flash one or more times to indicate the second digit of the trouble code. Count the number of times the lamp flashes to retrieve the second digit.

5. If more than one trouble code is sent:
a. Following transmission of the second digit of the first code, there is a 3 second pause in which the lamp is off.
b. Once all codes have been sent, the data string is repeated. When you have recorded the same trouble code twice, it is an indication that the transmission has been restarted and that all trouble codes have been retrieved.

IMPORTANT NOTE ..If diagnostic test wire is installed across Pins 1 and 2 on connector in lieu of a Scanalyzer, the ECM is placed in a diagnostic test mode and the engine will start. The test wire must be removed from the data connector and the ignition switch turned OFF or the check engine lamp will continue to flash codes. A historic trouble code resides in the memory of the ECM until the code is cleared by use of the Scanalyzer or a total of 50 trips has elapsed. A “trip” consists of a start and run cycle, the run cycle lasting at least 30 seconds. After the 50 trip retention period, the trouble code is automatically erased from memory (that is, assuming no subsequent faults of the same type are detected in that period). The numbers after the 'historic' or 'current' is the speedo code number, but without the electrical diagnostics manual you're not going to know what they mean.

The code numbers are the numbers that appear in red.

1 Current 53 ECM flash error
2 Historic 53 ECM flash error
3 Current 54 ECM EEPROM error
4 Historic 54 ECM EEPROM error
5 Current 63 ECM serial data low
6 Current 63 ECM serial data open/high
7 Current 63 TSSM serial data low
8 Current 63 TSSM serial data open/high
9 Current 61 Loss of TSM/TSSM serial data
10 Current 14 Loss of all ECM serial data (state of health)10 24 Loss of vehicle speed10 33 Loss of vehicle inhibit motion10 43 Loss of powertrain security status
11 Current 33 System relay contacts open
12 Current 33 System relay coil high/shorted
13 Current 33 System relay coil open/low
14 Current 33 System relay contacts closed
15 Current 99 Incorrect password
16 Current 99 Missing password
17 Current 41 CKP sensor intermittent
18 Current 41 CKP sensor synch error
19 Current 11 TP sensor open/low
20 Current 11 TP sensor high
21 Current 12 MAP sensor open/low
22 Current 12 MAP sensor high
23 Current 14 ET sensor voltage low
24 Current 14 ET sensor open/high
25 Current 15 IAT sensor voltage low
26 Current 15 IAT sensor open/high
27 Current 24 Front ignition coil open/low
28 Current 25 Rear ignition coil open/low
29 Current 24 Front ignition coil high/shorted
30 Current 25 Rear ignition coil high/shorted
31 Current 24 Front cylinder combustion intermittent
32 Current 25 Rear cylinder combustion intermittent
33 Current 23 Front injector open/low
34 Current 32 Rear injector open/low
35 Current 23 Front injector high
36 Current 32 Rear injector high
37 Current 16 Battery voltage low
38 Current 16 Battery voltage high
39 Current 43 VSS sensor low
40 Current 43 VSS sensor high
41 Current N/A (no speedo code for this) Check engine light open/low NO CHECK ENGINE LAMP AT KEY ON or CHECK ENGINE LAMP ON CONTINUOUSLY
42 Current N/A (no speedo code for this) Check engine light high NO CHECK ENGINE LAMP AT KEY ON
43 Current 35 Tachometer low
44 Current 35 Tachometer high
45 Current 25 Rear cylinder no combustion
46 Current 24 Front cylinder no combustion
47 Current 34 Loss of idle speed control IDLE AIR CONTROL
48 Current 35 Accelerometer fault
49 Current 34 Starter output high
50 Current 25 Ignition enable output high
51 Current 21 Left turn output fault
52 Current 22 Right turn output fault
53 Current 11 Battery voltage high
54 Current 31 Alarm output low
55 Current 32 Alarm output high
56 Current 41 Ignition switch open/low
57 Current 42 Cam position sensor
58 Historic 63 ECM serial data low
59 Historic 63 ECM serial data open/high
60 Historic 63 TSSM serial data low
61 Historic 63 TSSM serial data open/high
62 Historic 61 Loss of TSM/TSSM serial data
63 Historic 14 Loss of all ECM serial data (state of health)
64 Historic 33 System relay contacts open
65 Historic 33 System relay coil high/shorted
66 Historic 33 System relay coil open/low
67 Historic 33 System relay contacts closed
68 Historic 99 Incorrect password
69 Historic 99 Missing password
70 Historic 41 CKP sensor intermittent
71 Historic 41 CKP sensor synch error
72 Historic 11 TP sensor open/low
73 Historic 11 TP sensor high
74 Historic 12 MAP sensor open/low
75 Historic 12 MAP sensor high
76 Historic 14 ET sensor voltage low
77 Historic 14 ET sensor open/high
78 Historic 15 IAT sensor voltage low
79 Historic 15 IAT sensor open/high
80 Historic 24 Front ignition coil open/low
81 Historic 25 Rear ignition coil open/low
82 Historic 24 Front ignition coil high/shorted
83 Historic 25 Rear ignition coil high/shorted
84 Historic 24 Front cylinder combustion intermittent
85 Historic 25 Rear cylinder combustion intermittent
86 Historic 23 Front injector open/low
87 Historic 32 Rear injector open/low
88 Historic 23 Front injector high
89 Historic 32 Rear injector high
90 Historic 16 Battery voltage low
91 Historic 16 Battery voltage high
92 Historic 43 VSS sensor low
93 Historic 43 VSS sensor high
94 Historic N/A Check engine light open/low NO CHECK ENGINE LAMP AT KEY ON or CHECK ENGINE LAMP ON CONTINUOUSLY
95 Historic N/A Check engine light high NO CHECK ENGINE LAMP AT KEY ON
96 Historic 35 Tachometer low
97 Historic 35 Tachometer high
98 Historic 25 Rear cylinder no combustion
99 Historic 24 Front cylinder no combustion
100 Historic 34 Loss of idle speed control
101 Historic 35 Accelerometer fault
102 Historic 34 Starter output high
103 Historic 25 Ignition enable output high
104 Historic 21 Left turn output fault
105 Historic 22 Right turn output fault.
106 Historic 11 Battery voltage high
107 Historic 31 Alarm output low
108 Historic 32 Alarm output high
109 Historic 41 Ignition switch open/low

 

Thanks for the info. I forgot to mention that the bike is carb'd. Not sure if it changes the diagnosis (probably does).