Hi Jim,
Good news, sort of... I did get the new plug leads fitted yesterday, we had an uncharacteristically good day for winter - clear blue skys and sun nearly all day, dry ground, and rising to a balmy 5 degrees by mid afternoon.

I couldn't let that go by without making good use of it.
While I had everything out I did a few additional checks to try to rule other things out and be thorough.
Rear spark plug wells were checked for oil - there is still a minor oil leak near the back rear on the cambox covers going into the right rear and middle rear cavities but not much...maybe a teaspoon at the most, and nowhere near going up the spark plug tube, so while that needs doing one day its not causing me any problems at the moment.
All spark plugs were removed and inspected, a slight bit of oil on the base of the thread on a couple (or maybe grease as I slightly greased the threads when I originally fitted them) but all the electrodes were in perfect shape, no signs of fouling, overheating etc.
I tested the compressions, and I THINK they're ok but I'd like opinions from people who have actually measured compressions before. Looking at the engine from in front of the car the readings I got were:
Rear Left: 221 psi, Rear Middle: 218 psi, Rear Right: 221 psi,
Front Left: 225 psi, Front Middle: 220 psi, Front Right: 219 psi.
As the gauge graduations were only every 10 psi there could be an error of about +/- 2 psi in the readings as I'm just having to judge the in-between values by eye...all the readings were a lot higher than I expected, I was guessing I'd see around 150psi, and the "green" range on the gauge is between 100 and 230 psi, (typical values for a variety of engines I guess) so it may be ok. Has anyone else taken compression readings on the ES9J4 ? They all seem to be within a few percent of each other anyway, there is no one cylinder with an obvious loss of compression.
Other things I checked was the resistance of the injectors - all were 12.9 ohms +/- 0.2 ohms, I cleaned the contacts of them as well - why not when they're right there easy to get at with the manifold off.
I did find a slight tear in the rubber blanking plug that blanks off the spare manifold vacuum spigot near the throttle body, I don't think its actually leaking but I've had to leave it as is for the moment as I didn't have anything to replace it with. I want to put my vacuum gauge on there soon to do some vacuum testing so I'll have to find something new to act as a blanking plug as the original also has a crimped clamp.
I filed the sharp edges off the spark plug lead guides but STILL had a lot of trouble with them. The problem is that it seems to be nearly impossible to judge exactly how far through to feed the wires on the guide that runs over the back, either the plug leads at the front won't reach or they'll be too long with nowhere to go. Trying to readjust the position of the leads in the top guide without damaging them is very difficult but I got there in the end and I'm pretty confident that I didn't damage them this time.
Of course I fitted a new intake manifold gasket during reassembly. So is it fixed ? Sort of.
As soon as I started it after reassembly I could tell by the sound that the misfire was gone, the engine "burble" sounds quite different when running normally than when its misfiring, and there is no shaking of the engine on its mounts either - its dead steady.
A test drive was a little bit disappointing. Yes the misfire is gone, yes there is a lot more power, but there was still intermittent throttle lag and it's not going as well as it was the weekend that I drove to David's where it was literally going like a bat out of hell. I would judge that it's about half way between running poorly and running normally as it did that day.
There was still some hesitation at low rpm where you'd put your foot down a bit and it would muck about then suddenly pick up. When I drove it a second time a few hours later it was considerably better but still not perfect. Remembering another thread where someone solved a hesitation by replacing their oxygen sensor I disconnected the oxygen sensor again - and interestingly the hesitation when going from light to moderate throttle was largely eliminated, but there was still a bit of intermittent throttle lag. I've put the oxygen sensor back on again for now.
At higher speeds the performance seems fine, I was giving it a blast uphill along an empty dual carriage way and it had no trouble getting me very quickly to speeds that would get me in trouble.

There's plenty of power there when you open it up, but it's intermittently still reluctant to pull well at low rpm.
I do think my sluggish oxygen sensor could be causing some trouble and maybe is the source of that hesitation so I think that's next on the list in maybe a month or two... and I'll take the opportunity of having that out to do an exhaust back pressure test via the oxygen sensor port. I have a gauge, all I need is a long heat resistant fly lead/adaptor.
I did want to get the fuel pressure gauge back on the fuel rail again yesterday after coming back from my test drive to see if there was any drop in fuel pressure when the performance is worse (maybe its intermittent and happened to be ok the day I measured it) but it was just too late, cold and getting dark by then so I called it a day.
On the day before I drove to David's as well as taping up the hole in the spark plug lead I did the fuel pressure test - is there ANYTHING that testing the fuel rail pressure could have done to affect the running ? I did purge it a few times while the pump was running probably to the amount of a few hundred mls, but I can't see how this would have had any lasting effect.
So all in all, a mixed bag. Compressions look ok, spark plugs are ok, new spark plug leads are fitted, misfire seems to be gone, overall power and running seems a lot better but there is still something weird and intermittent going on, and it is definitely not performing to the same level that it was the weekend I visited David.