The dropping resistor pack on your car will be on the right side of the firewall, attached to an alloy plate that acts as a heat sink on which are also mounted the two ignition amplifiers. It is located behind and below the relay bank. The wiring on the 6.0 is different to an XJS and the dropping resistor pack is in a much more protected position, but by all means have a look at the condition of the plugs on all three modules.
The V12 is a very simple engine. Although the 6.0 is a generation newer than the 5.3 and has interlinked engine, ignition and transmission control modules, in many ways it is still much less complex than the six cylinder in the XJ40. For instance it has no idle control stepper motor and no air flow meters - it even has the same number of camshafts and valves as the six cylinder. It's just that the V12 has 12 of all of the simple components and therefore double the chance something will be missed that would get picked up on the six cylinder.
There are only three things that can cause a misfire - compression problems, ignition problems and fuel supply problems (including vacuum leaks, sensor problems etc) - just like any other engine.
You need to start eliminating some basics before getting into guesswork about injector wiring or anything else. If you don't have the equipment to do these very basic tests you need to find someone that will do them properly for you.
Do a compression test and get the actual figures on each cylinder. V12s almost never blow head gaskets but since your car sat around for a long time before you bought it things like sticking valves are a potential problem. The 6.0 runs smaller clearances than the 5.3 on everything, including the valve guide to valve stem clearances. I have seen plenty of stuck valves on 6.0s that have sat for long periods of time.
Next, pull all of the spark plugs and make sure each one has a good spark at the electrode. Make sure the plugs are all clean and none have black sooty deposits. V12s run relatively small spark plug gaps because of their very high compression and it doesn't take much to foul the plugs on a V12, especially if they are repeatedly run at cold start (i.e. being moved around a lot but not driven on the highway). Spark breaks down under compression (and V12s have high compression) so spark plugs and leads always need to be in very good condition on the V12.
Make sure you have good fuel pressure at the fuel rail and that your fuel filter is new.
Get a mechanic's stethoscope and check that each injector is ticking with the engine running, that will soon tell you if there is a wiring problem or a faulty injector. You can do the same test with a long screwdriver by placing the tip of the screwdriver on the injector and the handle against your ear. It is not as accurate but it does work. It would be better to use a mechanic's stethoscope though.
Listen with a piece of vacuum hose to the nose of the injector where it goes into each intake runner. The injectors on the 6.0 have plastic caps on them and these are prone to breaking up from heat and disappearing into the engine to be burned up. The injectors then have vacuum leaks around their tips.
If you do all of this and you find that one or two cylinders are still not firing properly (spark plug colour will tell you this), get the injectors cleaned and tested to make sure they are working as they should and replace them with new seals and plastic caps.
Check every vacuum hose and rubber blanking cap under the bonnet - there are lots of them. Don't assume they are okay because they look okay where they attach to the manifolds, if necessary pull them off to check their entire length. My bet is many of them will be rock hard and long overdue for replacement. The V12 has a very narrow range of fuel trim in the engine control ECU so lots of small vacuum leaks can quickly cause very lean running.
As mentioned previously, make sure the gaskets between the manifolds and the heads on each side are the correct thicker gasket. While you are there make sure all of the nuts holding the manifolds on are torqued correctly.
Somewhere in that series of tests you are likely to find a very simple problem that has been missed.
'94 XJ12 (and other toys)