Doing what? building an RS4 from what?
the issues you mention are the reason I didn't look at the S4 shell to fit my 2.0l 20v engine in. different loom, different ECU, different gearbox etc etc.
but if you were dropping in an S4 engine into an S4 body there is no issue.
If you speak to the MRC, UNIT20, Dialynx chaps they will tell you that they rarely fit RS4 engines to cars they are tuning for big power when they can fit S4 engines, or even better an S4 engine with NA heads. just too expensive to find an RS4 engine and for little gain.
(I only know this as a mate of mine asked me to find him an RS4 engine, he races one but doesn't do the whole forum thing and didn't too many people in the UK as he gets all his work done in Germany.)