I have a 2000 BMW 528i with 200k miles on it, service engine soon indicatir came on however everything seems to be running great. Could this be just air cleaners replacement or similar? Would rather not go to dealer if I can eliminate myself.

without a scanner, you are lost- just take it to a mechanic- the days of "fixing your own" are over- you cannot "cheap out" any more- with that many miles on a BMW expect a lot of scanning- rethink the problem

Scanner reads: A I R D Secondary air injection pump What is the function and is it difficult to repair?

That is an emission system for your vehicle. Most likely you will have to replace the system, pump and valve. Basically moisture gets in the system and ruins it. But do be sure to check the vacuum line running to the valve itself I see a lot of times it get weathered and causes a vacuum leak. Here is a link all about this system. http://www.bimmernut.com/forum/5-series- bmw/43760-secondary-air-pump-sap-troubleshooting- repair-2000-bmw-e39-528i.html