hi robjohn
I had the idle speed problem too does your gear stick and seat shake abit, when you open the engine bay the engine block is shaking, when I had my dakar yellow compact took it Menzies bmw in Stirling twice where I bought it they told me the twin cam M44 engine is like that....
I then took it to easten in Edinburgh where they told me the M44 engines latter on had its cam timing changed authorised by BMW as a important change, and my car slipped through the systems. To cut a long story short I had to pay £200 to get it done because my X 2000 compact only had the one year warranty and it expired 3 months ago.
The end result it was ok for 2 months and the shaking re-appeared again, by than I was too pissed off and was going to modify my car alot so wouldn't have much of a case later on to get them to fix it (chip, ram air induction kit, exhaust, short shift, adjustable roll bars, springs, bike cam exhaust) so just left it in the knowledge another BMW garage ripped me off....
But I have sold the car now with 25,000 miles and it still shakes and idles poorly but i soon got use to it and stopped thinking about it i don't think it will cause any damage because I've driven it for about 15,000 miles with the idle problem....
As for the exhaust not sure changed mine to bike cam exhaust, regarding the stalling I had to problem abit when I started it in the cold or left the car for a week without driving it had to call out the A&E bmw services to get my car started. The friendly chap told me the M44 engines don't have the systems like the E46 models to vary the start up (something on those lines!!!)
I hope this helps i understand your problems, I loved that motor it attracted so much attention I miss it just replying to this post...
Take Care
Chrisss