Alright, everythings been sorted.
I disconnected the battery and went through the harness connections. The original loom was not screwed in tightly so I did this up. I also went through the wires and found that all were fine. Reconnected the battery and fired her up. Took her for a spin and shifts were perfect again.
It actually felt smoother than before the eManage. I think that I should have reset the ecu after installing the shift kit as well! Anyways, so far so good with the eManage but still early days. I'll post up the condition of my coils when I change the spark plugs next. I've got a set of backup Splitfires in case they melt.