That could be just low battery.

With regard to the engine knock, it will always appear if one (or more) cylinders are not firing. So, you will first need to do an OBD scan to determine whether any (and which) cylinder is misfiring.

If all cylinders are firing, you may consider replacing the conrod bearings (provided there is no visible damage to the crankshaft journals) which can be done in-situ - with quite a bit of parts removal, including the timing cover and the front crossmember. The conrod bearings are colour coded and you can find which colours you have on a stamp at the side of the engine block:


This example shows that the conrod bearings are *ABAA* or Blue-Green-Blue-Blue in the order front to back of the engine (crankshaft).

 

How easy is this to diagnose? I was already on the fence on whether it was worth it to spend the money rebuilding the heads, at this point it's starting to feel like throw good money after bad.

 

First thing, as I mentioned, is to make sure that all cylinders are firing. The knocking may disappear if you find some misfiring and fix it by replacing the offending ignition coil or possibly just the spark plug (but, in the case of detected misfire, it is more likely the ignition coil).

If you still have the knocking once you confirm that there is no misfire on any cylinder, while the engine is idling, engage the transmission into drive (R or D, brakes on) and note whether the knocking almost disappears. You can also test with the AC on (compressor engaged) and the transmission into drive to provide more load to the engine. If the knocking sound changes significantly between no load and the described load, then it is one (or more) of the conrod bearings.

While having the knock at idle, you can also try revving the engine a bit (say, up to 2000 rpm) and see what happens with the knock.

However, the crank bearings are rarely damaged by overheating (and more by loss of oil pressure) so you should first concentrate on eliminating misfiring (if any).

 

If I'm understanding you correctly, you are suggesting its the spark plug or the coil pack? I've already swapped out the fouled plugs for new ones only to be left with and engine failsafe message on the dash and the car not starting. The possibility that all four coil packs on the same side of the engine failed seems, well, optimistic. I'll swap the coils with the ones on the driver's side and see if the mis fires move to the other cylinders, but I'm not hopeful.
As for the knocking going away, the trans high temp fault prevented me reving the engine over 3000 rpm but as the engine reved up the knocking went away.

 

So I swapped the coil packs between the driver's side and pass side. I also checked the battery, it read low 12.09 volts, but I don't know if thats from cranking it over and over yesterday while doing the compression test and subsequently attempting to start it after that. So while I was swapping the coil pack I put the battery on a trickle charger. I tested it before putting it back in the car and it read 12.2V still low. I'm going to slow charge it overnight, unplug it in the morning and then check the voltage when I get home from work tomorrow.
Anyway as for the motor, it started right up but the knocking was more pronounced. I shifted into Drive and it immediately threw a trans fault and went into limp mode. I let it idle waiting for it to throw a CEL but with the knocking so bad I didn't want to leave it running too long. Checked my code reader and it had pending codes for p0399, p1316, p1000, & p0705.
Not sure if any of this means anything but this knocking did not sound good, I'm even less optimistic about this motor now. Here is a video from today:

 

The engine now sounds very much as if it is misfiring on 2-3 cylinders.

P0399 - This is not a Jaguar specific code; seems to be caused by some ignition problem

P0705 - Transmission Switch circuit malfunction; this is caused by low battery or low alternator voltage

P1316 - Misfire, Ignition Coil failure, Spark Plug failure; this code will appear if you also have one of the P0301 to P0308 which tell you which cylinder number is misfiring (P0301 for Cyl.1, P0302 for Cyl.2 etc.)

The code P1000 you got means that your OBD check is not complete. You should read the codes again and, hopefully, get some of the P0301 to P0308 codes to know which cylinders are misfiring. If you still don't, try with another code reader. If you have not already changed the spark plugs, perhaps you can first try with new ones.

 

The fouled plugs from yesterday have already been swapped for new ones

 

So tried to investigate thing a little further today. I left the battery on a slow charger since last night and took it off the charger once I got home from work. I left it sitting off the charger for an hour and checked the voltage 12.6V a little bit low but still a good battery. Then I put it back in the back and went to start it. Immediately the car would crank but not start and was displaying failsafe engine mode on the dash. I thought this was weird because with the battery removed for 24 hours then it would not have any stored memory. I did get the car to start by putting it the trans into neutral, and let it idle for a little while. Again I could not get it to throw a CEL but I tried scanning the codes again and got pending codes for p0305, p0306, p0307, p0308. The CELs it was throwing before were for p305 and p0307 so it seems moving the coil packs did not move the misfire. That makes it safe to assume the problem was not the coil packs.
Also I pulled the spark plugs on that side and they did not appear to be fouled, they did not have the carbon deposits it had before.

 

Obviously, you have serious misfiring so forget about the conrod bearings for the time being. As the first (and cheapest) step, I would replace all spark plugs with new ones (replacing only a few fouled ones is not the way to go).

Otherwise, your detected misfiring on cylinders 5, 6, 7 & 8 is not all on one bank. See the diagram below for the cylinder numbering.

 

I only replaced the ones on one bank because the ones on the other bank looked fine. In fact they still looked brand new.

But looking at the diagram has me more worried now because the cylinders missing we're the same ones that dropped the valves when it over heated.

 

Perhaps your spark plugs are fine then. I would suggest that you now move the coils 5, 6, 7 & 8 (the rear 4, 2 left, 2 right) to the front cylinders 1, 2, 3 & 4 and put the front four to the rear of the banks. Run the engine and listen to any change in sound (knocking). Then, scan again to see what misfire codes you get.

Otherwise, the type of ignition coils you have (4 wires) are more susceptible to failures than the early 2-wire coils as the 4-wire coils also have some electronics inside. Engine overheating could have damaged their electronics.

 

I just read your old posts in this thread. If you could undo the crank pulley bolt with this tool, then the bolt was previously torqued well below the specified value. In any case, the question now is how did you hold the pulley to tighten the bolt. The specified torque is very high, 375 NM or 275 Lb.Ft. The only way to achieve this is by using the Jaguar special pulley holder (or its equivalent). If the pulley is somehow sufficiently strongly held by a tool that clamps the outside of the pulley, then you risk damaging the rubber insert (vibration damper) as it will be exposed to very high torque (shear forces).

I also read your write-up about installing "new" cylinder heads. Did you use new head bolts?

Perhaps you wrote about how you did the above two things in other threads on the same subject but I have lost track so I am asking these questions just based on this thread.

 

Moved the back four coil packs to the front four cylinders, ran the car, it idled with the knocking still and the trans fault. Code reader came back with p0300, p0305, p0307, p0705, and interestingly now I've got p0102 Mass Air Flow Circuit low input and p0112 Intake Air temp sensor circuit low.
I cleaned off the MAF sensor with MAF clean when putting everything back together, and cleaned it off again after starting and getting this knocking. I should note that I do not currently have an air filter in the airbox but otherwise the air intake is assemblyed and hooked up correctly. I wouldn't think an air filter would mater anyway since the MAF meters the air after the air filter.

I did use that to immobilize the crank. I wrapped it around the pulley and used a breaker bar to turn the crank bolt. To tighten it I used that same tool with a cheater bar over the handle to hold the crank pulley and a torque bar to turn the bolt. My torque bar maxed out at 250ftlbs so after reaching that torque I attempted to turn it with a breaker bar but was unable to get it any tighter.

I did use new head bolts, and new head gaskets.

 

P0705 (Transmission Switch), P0102 and P0112 could all be caused by low battery i.e. low alternator charge. Start the engine and measure the voltage on the battery posts. If you get less than 13.5 volts, you will need to rebuild the alternator.

 

I'll check that tomorrow, but that couldn't cause the misfires.

 

Low battery (alternator) voltage will cause numerous "fault" codes even though the components are actually good. Making sure that the alternator produces 13.5 to 14.2 volts measured on the battery at idle is crucial. Then chase the actual fault codes.

 

Yes but I'm not getting some phantom fault code for miss firing. It really is miss firing. The trans faults don't actually worry me at this point. If I've got a junk motor it doesn't matter what faults the trans is throwing.

 

Sounds as if the timing is off.

 

Could be. But why would only 4 cylinders be off? With the timing tool set I can't see how you could mess up the timing.

 

Checked the alternator just now, it jumped from between 13.35 and 13.57 so just out of the range, but this is with it idling on only 4 cylinders.