A bit of an update -
I took the car to Vocky to take a look at the wiring. He stripped out the engine bay loom, tested it and re soldered all the extended wiring used for the supercharger conversion. He also tried a known good coil pack and some other spark plugs. No real difference noticed.
He then tried a different coolant temp sensor and there was a slight improvement so he installed a new one. I used the journey home to re-learn the base fuel table, which was about an hour and half of solid driving at varied speeds, loads and gears, mostly trying to focus on the problem areas wherever I could. The stuttering is considerably better, but certainly still there, particularly when gently trying to increase speed from around 2k rpm and is still there when the engine is under no load at all i.e. in neutral just holding the revs at 2k.
In total, the car has had replaced:
coil pack
spark plugs
ignition condenser/suppressor
ECU
complete bottom end
head gasket
valves
valve stem seals
cams
inlet/exhaust gaskets
complete exhaust system (3" tullett + HSJ cat)
injectors
fuel pump
throttle body
Both OEM O2 sensors
2 wideband O2 sensors
crank sensor
coolant temp sensor
knock sensor
two timing chains (most recently timing set by Vocky)
During the stuttering the fuel pressure reads constant and normal and the lambda reads constant and normal.