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KJ 119,
based on your results you completed and understood the point of pinning out the harness, to check if any of them are grounded or shorted between the ecm connector and the injector it'self.
I would 100% swap the ecm if possible as it is a very suspect part at this time.
There is no way that three cyl will suddenly drop compression to the point that they will not fire. Since you have the injectors out use a borescope to check the condition of the liners. If they have a large amout (or any, really) of adhesive wear, that could drop compression significantly, however that would be the result of some other failure, and your non firing problems would at that point be a non issue.
If i were in the shop with your engine (say it came in just like it sits on a tow truck) I would install the tested injectors, disconnect the airbox from the turbo inlet and unplug the glow plug relay harness, I would then attempt to run the engine on ether/starting fluid. If the engine runs on ether then you know it's not a timing issue. After a few moments on ether you can check exhaust manifold with a ir thermometer to look for dead cylinders.
If it does not run on ether you have a timing problem.
During this procedure i would examine the return fuel, looking for excessive air, i would also install a gauge to check rail pressure. (may have to remove the factory sensor)
If rail pressure was not developed to spec (you have to have a minimum pressure to unseat the nozzle at the tip of the injector (called nop), i don't know what that pressure is on the crd, but since the bosch guys said the injectors were good, they are good) then you have a issue with fuel rail pressure (obviously) it is unlikely to be a nop issue because one injector does (did) fire correctly.
I will assume that you have already checked for fuel inlet restriction with a manometer (or similar)
A plugged fuel filter can cause the problem your having but it is usually not so immediate. especially considering that it runs on one cyl,
however i once had a m-11 come in and the first thing we did was swap the fuel filter (standard procedure for hard to start complaint) it proceeded to run on ether and only fire (diesel) on one cylinder.
I swapped the injectors after checking the harness and so forth, that means i removed the overhead removed the injectors and installed known good injectors, reinstalled and ran the overhead, etc etc, guess what? same result. i pulled out the manometer and i had inlet restriction (remember it ran on one cylinder). I was using my own fuel tank and lines (disconnected the chassis lines) so i knew it was not my test equipment. Swapped the filter AGAIN. Started right up. Can you believe that? So i put the customers injectors back in. I only billed him 3 hour. It took me about 6. it's a HUGE pain in the booty to remove the injectors from a m-11 because of the way the rockers and push tubes are set up, you have to set the valve lash (obviously) and since the train is three piece you also have to set the clearances between the rockers themselves. They also have a really pita torque sequence. I never cut the filter open to see exactly wtf was going on (at 150 an hour who would?) I went on to the next one. I've swapped injectors/run the overhead on m-11's so many times i could do it sleeping, I am very intimate with m-11's so it was "easy work"
I work on diesel engines and heavy equipment and the above work would have been preformed before sending the injectors out or testing the harness (not the injector swap but the manometer and ether and return fuel check etc).
On a normal heavy truck these procedures take very little time however on the crd they are not trivial.
In your case simply changing the fuel filter would be the first thing to do but that does not mean that you do not have inlet restriction pre filter, such as the fuel strainer in the tank.
Anyway i thought i would share that frustrating experience with you.
1. change that fuel filter if you have not already
2. swap the ecm if you can
3. keep trying, you have done thousands of dollars worth of work already, and you have learned a lot. I don't think a dealership (jeep) could have done any better, yes you have done some things out of order and wasted some time, what of it?
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06 CRD Limited. IMII, GDE TCM, Carter transfer pump, Upgraded oem primary, 2 micron secondary, 3 inch mandrel straight pipe.
Transgo shift kit, EHM, fcv butterfly removed, egr plated off. 19 3/8 solid flex fan, no electric fan, 10k lb aux trans cooler.
Frankenlift II, Mopar skids, allj's rails, 235/85 km2 on stock rims
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,now we know where all that GDE cash is going. 
) and vacumed,installed injectors with new copper washers and o-rings,torqued bolts to 24 ft#(seemed miniscule compared to the torque to remove),hooked up all lines and tightened.
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