This is of course one of the more daunting aspects of a conversion and information is often hard to come by. The engines come with there own looms which plug into the main vehicle harness to cover all the ECU's requirements and any power feeds required (such as HEGO/Lambda sensor power supplies) and signal outputs (Rev counter signal, coolant temp sensor signal etc...). Depending on which vehicle your loom came from it could have either one large connector (Mondeo) or two smaller connectors.
One thing to note, if your donor was an automatic then you will find that you have a rev limit as without the gearbox feed it will think it is in neutral. There is likely a pin that can be shorted to earth to overcome this but as the ECUs are obviously configured differently I don't know if the maps might also be different to better suite the characteristics of the automatic transmission.
The following is all based around the loom that I used ('98 Mondeo 1.8 LX 'Silver-Top') but should be common to most. All required connections are made via the large black square 42 Pin vehicle loom connector with the exception of two separate power supplies, one for the PATS (Passive Anti Theft System) Transponder Ring and one for the admittedly optional fault diagnostic connector also known as the Data Link Connector (DLC).