Your wiring loom is probably pulled out a bit on the plugs. They don't service them anymore so your best hope is to have a look and see if there's any loose wires or pins pulled out that are obvious and fixable.
I have a 1999 TL1000s setup with a Smart TRE and it runs fantastic, starts up 1st time every time no loss of power anywhere no complaint at all the PCIII has never let me down. If I remove the PCIII bike runs like SH*T but you need a good map!
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