You've got the right idea, start with the cheap stuff, it is usually something simple. You've already checked some of these but this list should be pretty comprehensive. Appologies for any repitition.
Check here:
BMWE34.net
and
Rough Idle
Haynes manual also suggests:
Vacuum leakage
Air filter clogged
Fuel pump not delivering enough fuel
Leaking head gasket
Timing belt/chain and or sprokets worn
Camshaft lobes worn
Faulty charcoal canister (Part of EVAP system, Usually only fitted to cars with Cats)
Could be fuel injection system:
Idle air stabiliser valve faulty
No power to idle air stabiliser valve (Check relay and wiring)
Vacuum advance system faulty (check system and electronic V.A. relay
Idle speed control unit faulty (Dealer check)
Be lucky!
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Hartge 535i Sport - 230,000 miles and going strong