Sounds like a buggers muddle to me...
The piecing it all back together; if it were me I would make the carb work properly, i.e. buy a Mikuni and an ignition unit such as
this. This will give you very good results as I run it on my S1.
Alternatively, its a case of trying a different ECM and a different fuel pump, loom and anything else that doesn't appear to be working. Have you checked continuity from the ECM pin for the Check Engine Light and the bulb itself? Likewise for the fuel pump? You are welcome to send me your ECM content (download with ECMSpy) and I will have a look to see if there is anything that has been changed.
The plug; I am not sure where you would buy one easily apart from cannibalising another loom although it is a common item used on a lot of Fords.
This manual may help.