Hi mate,

I've just finished doing something very similar, i dropped a S2 RST lump into my mk5 (albeit tintop). I think you'll find it easier to find any problems if you pull the mk4 loom apart and just keep the parts that run the engine. On mine i ended up splicing the RST loom parts onto the mk5 engine loom connector so i can take the whole lot out.
Bearing in mind all the engine needs to run it is power to the ecus and fuel pump (and some sensors and stuff) and a cranking feed it ends up being quite a small loom.

MazakMan