You have done well in addressing a number of problems. Given what you have reported in your latest post, I will offer some suggestions. These are things I would look at if it were mine, but they are by no means gospel.
Replaced vacuum lines today as they were starting to split - no change.
Checked plugs & they were wet with fuel which I expected as it is misfiring, gaps were fine tho.
You say you saw no change with the new vacuum lines. Did you retain the four small plastic jets inside vacuum lines? I can't say if their impact is significant, but when it comes down to fine tuning the idle, those jets may be an influence. However, even if they are gone, I don't think their absence is the primary issue with the lumpy idle.
Fuel-soaked spark plugs can fail and/or cause poor performance. Difficult to say if yours are at that point, but it is good to keep this in mind if all else fails.
Put a multimeter on the battery & it was at 12.5v, turned ignition on & voltage slowly dropped to 12.2v, started the engine & voltage picked up to 12.4v and didn’t move despite raising the revs. I was hoping it would go up to 14v!? Wondering if it’s worth buying a new battery.
Dunno if this may be linked but both of my headlights had blown, prior to this testing.
Headlight bulbs fail from age, vibration, and over-voltage. The voltages you measured were not excessive. In fact, the system voltage is lower than it should be, and this is the real indicator of a problem. The TL OEM charging system is not great. There are weak links in the circuit that cause it to underperform and even fail. The voltage at the battery should be at least 14 volts at 5K RPM. The voltages you measured are typical of a system that needs attention.
If you haven't seen it already, read through this thread in the Frequent Mods forum. It explains the flaws and the fix for the charging system. While most of the problem is in the OEM wire loom, many members have upgraded to a MOSFET rectifier/regulator (because it is more efficient and runs cooler), but the OEM SCR regulator will do the job if if is functional and the wiring is improved.
Definitive Charging System Diagnostic & Upgrade Thread
A battery that is perpetually under-charged doesn't perform at its best. It makes for difficult starting and a weak spark at the plugs. This may or may not be impacting your idle issue.
Also, I read on here a way to check reg/rec stator is to unplug the reg & see if the bike runs. It did but still lumpy, backfiring & wanting to cut, so from that I think they are ok.
Can anyone spot an obvious issue?
Just to rule the fpr out I’m going to test the pressure at the banjo bolt on the manifold.
When the stator is disconnected from the rectifier, the electrical system is completely reliant on the battery. In your case, the battery is only at 12.4v (or lower with the R/R disconnected), so that likely explains the poor engine performance.
If the battery is more than two years old (and since it has never been charged properly while in your TL), it is probably best to replace it (and fix the charging system).
You posted previously that the fuel pressure directly from the pump was great, and that's good. The fuel pressure regulators (FPR) rarely fail, but it's good to check the fuel rail pressure if you have the tools. Then you can cross it off your list.
I haven’t messed with the TPS yet as I want to rule out as much as I can before I interfere with it. I did start it in dealer mode & the marker stayed at the lowest point even under revs....
I think you have ruled out quite a few potential problems already, and now it is time to play with the throttle body balance and the TPS.
I say this for two reasons:
1) You have found that the TPS does not respond to throttle movement as it should. The 'dash mark' in the LCD window is not centered but stays on the low side. Therefore, something has changed.
2) The TB balance greatly affects the nature of the idle. You will see as you adjust it. The slightest movement of the adjustment screw can make the idle purr, go lumpy, or fall on its face.
You may need to go back and forth between the TB Balance and TPS adjustments to get it where it needs to be, but just remember to adjust the TPS last.
I'm looking forward to hear what you find.