Will a 1994 engine work in my 1991 XJ6?

Came across a 1994 engine and transmission local to me, wondering if it would be a direct swap into my 1991 XJ6?

If the spark plugs are fired by wires the same as your ‘91 then I can’t think why it wouldn’t work but it must be close to the change over to the AJ16 engine with coil over spark plugs.

There are a few differences.
The injectors are ‘green-band’ but should work OK with the ECM.
The oil filler and crank-vent systems are different. (but should cause no issues)
Heater control valve on the later engine but not needed unless you add a red plastic line to the vacuum valve block.

Might be a few more I can’t remember?

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Purchased a 1994 engine and transmission for $50, was told had about 67,000 miles on it but hasn’t ran since 2008. Hopefully I will be able to do something with it! Giving myself 5 months

I’m still not understanding why you are considering “replacing” the engine with an unknown engine, when you haven’t really diagnosed the issue with the current one. You’re replacing your house because your toilet’s not working. SOMEWhere there is a fault that can be rectified.
Clearly from your video and descriptions you are able to start the car, and keep it running by revving it. Spark and fuel delivery are there, just off. You say you’ve done the timing correctly twice now?
Since you have this “new” engine - do you now have a second set of components? You could try swapping out parts to test - the distributor including cap and rotor, the crankshaft position sensor, fuel pressure regulator, the idle air control valve, throttle position sensor.
Doing this will save you a ton of time and effort before you go swapping out an engine.

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have you done a compression test? Do a compression test on all cyclinders to make sure you have compression on all of them. If you bent a valve trying to correct the timing after the head gasket, you’ll discover it.
did you replace the distributor and coil? Remember, “adjusting” the distributor by loosening the nut and turning does NOT do anything to change timing. Timing is controlled by the ECU.
Firing order. Double check you haven’t switched up two spark plugs wires? Perhaps 3 and 4 are backwards on the wires, so you’d only be running on two cylinders. Look at the firing sequence and make sure.
check for spark on all 6 - i know you can’t keep it running without reving, but you can see if disconnecting the spark wires one at a time changes anything.
One the intake side, make sure you haven’t separated the flexible bellow at the throttle body while you were doing the head gasket job. That could be an air leak behind the Mass AirFlow.

You should keep your other thread open, i had to jump between the two to remember you’d done a compression check previously. And replaced the distributor and rotor.

i would still use parts off your “new” engine to “swap diagnose” your old one.

Thanks Jitneybead for the words, your completely right. I need to try to fix the engine that is currently in it. It’s just super frustrating knowing it would have been cheaper by just taking it to a professional in the first place!

On a positive note the engine that I bought has some good parts like the oil cooler bypass that I can use

You don’t need the oil cooler bypass. Just clean up the face of the block and bolt the filter head to it using shorter bolts.

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I’d forgotten that you’d done the jb weld repair on the head and that you’d taken apart the valve train to do that repair.
I think you should take the head off the “new” 4.0 and put it in your engine and try again, this time without messing with the head other than taking to a machine shop. Spend your money on having them go over it for plane and doing a valve job.