bodged wiring, shoddy fabrication etc. it looks like a lot of stuff got rushed to get it working and a "that'll do" attitude rather than attention to detail.
With the wiring you need to transfer basically anything connected to the ecu (or at least consider it) so that the ecu doesnt know its not a focus. youll need to sit down with the wiring diagrams and compare the subsystems of both cars.
A GEM is just a electronic module. On a lot of later fords a lot of fusebox and relay functions were integrated into microprocessor controlled circuits. Saves space, more reliable and allows more modern features. eg on your frp, the early pumas would have had a basic electrical fusebox that connected to the ecu and an alarm module and an aux warning module etc with a whole load of relay controls. The later pumas the whole car fuse box was replaced with a GEM that replaced all but 2 relays from the central junction box. it also combined alarm unit and aux warn module all into one PCB.