OK..these wiring diagrams are the cause of my near baldness!!
If you have downloaded the 2006 Jeep KJ Service Manuals you will use Section 8w for the wiring diagrams. The Index section will tell you to go to Page 8W-21-3 for the M/T Starting System.
Unfortunately for the Diesel this Page 8W-21-3 does not show the Clutch Upstop Switch Signal connection!
I realize that putting the Transmission into Low is supposed to let you turn over the motor without using the clutch and you did state that this did not work!
Then go to Page 9 - 1101 for the diagram of the ECM input and Output wires that we are interested in....section 9W gives a larger picture but no Diesel Switch wiring.
I realize that you did try starting with Transmission in Low and that did not work but do the test of the switch as below in any case...we can test the outputs from the ECM to the ASD Relay and Starter Relay while operating the clutch switch.
If you go to Section 6-20 it gives you a description as to how the switch works...it tells you to measure the wire coming off the switch with an Ohmeter---Switch Depressed should be Continuity and Switch in a good mood ie. Released, should be No Continuity!
So first check these wires and try shorting them out....make sure you are in Neutral!!
The Wiring Diagram that does show the wiring for this switch is on Page 9 - 1101.
Make sure Fuses #6, #28, #18, #14, #26 and #8 are OK.
Now to test signals. The female pins on the ECM are pretty delicate so avoid putting a meter probe into them. I normally tape small pins or needles to the meter probes so that I can piece the insulation of the wires to make measurements...a dab of glue will cover up the holes when finished.
Place one lead on ground and test if pin #86 on the Starter Relay has +12 volts on it when Turning Ignition key to START.....should be there if Ignition Switch is OK and Fuse#28 is OK!
Place one meter lead on +12 volts right at the battery terminal and the other lead on pin #85 and turn Ignition key...supposed to show -12 volts ie. the ECM has supplied Ground to Pin #85.
Do the two above actions while operating the Clutch Switch and the Ignition to Start.
I believe at this stage the ASD Relay should activate....do the same measurements on the ASD Relay to see if it is energizing and supplying voltage at pin #87.
I had a problem on My CRD with the ASD Relay not energizing due to a broken wire...you can remove the Cover on the ASD Relay so you can watch it to see if it energizes!
If all the expected readings are there....we need to trace them down to where they enter the ECM...may be a bad connector or broken/shorted wire between the ECM and the two Relays. This is when you need to piece the wires just as they come out of the ECM C2 Connector with respect to Ground in some case and to +12 Volts in other cases....try both Ignition Keys!
If there is voltage/ground missing somewhere...isolate the leads by disconnecting leads C2 and relevant fuses and measure the ends end to end for continuity and seeing as they should be floating in mid air....no shorts to Ground!
A decent Code Reader or the Agent's Code Reader could pullout Error Codes.
If you get some codes the bottom of the Index Page has the DTC Index...find those codes in the list and go to the page called out.
The newer CRDs I believe Code Readers are available...our USA friends may be able to help you. The Export 2002/3 CRDs like I have does not have a Code Reader available...only Dealer Reader can pull the codes. This is because the 2002/3 uses only a PCI Bus and no Code Readers are available.
On my Export 2002 CRD I could only pull some codes out using the "Key" method but that does not work on the 2006 CRD!
Edit to Add: This is probably a SKIM problem ie. the Anti Theft.
Section 8J-135 and 8J-69 gives a description of how the system works.
They do state that to erase a SKIM light you must perform the Cluster Check Procedure!
Try this with both keys:
Firmly press in and hold the Odometer Reset plunger on the Cluster.
While holding this in, turn ignition ON but not to the Start position.....the lamps will flash On and Off a few times and all the gauges will swing back and forth.
This is not a test of the Cluster but merely a way to check all LEDs and Gauges are working and apparently it should clear any Red Led for the Skim system.
The test ends with some numerals and digits displayed....this is just the Firmware level of the Cluster.
Have fun!