I'm surprised your MKII didn't get the codes from a standard OBDII reader... our older ones have to go full T4 equivalent 
glad that the swap over of the controller seems to have done the job for you - I changed the whole pump over when I had tractor syndrome all those years ago at the pub meet!
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Mods Fitted
Pipercross Filter; Full 2.5" 'Wingy' exhaust; Donny Custom Turbo outlet pipe; Custom injectors;
Uprated gearbox bearings; Helix Clutch; Quaife ATB; Upgraded clutch Hydraulics; FMIC; Ported Head; ARP headstuds; Leda coilovers; 'Brembodge' 326mm disks/DS2500 pads
Dieselpowered
Fitting Custom Hybrid Turbo (1856GTBv) & controller; Remap, swirlpot, lift pump
AMW Motorsports
Custom exhaust manifold & downpipe
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