I had mine done a few years ago, theres a bmw workshop in town that has the lifetime fluid in their trans flush machine, budget at least $300, but when i did mine it was worth every dollar. You can / should drop the sump pan off the box and chuck in a new filter and gasket at the same time, only another $60 or so from memory.
Sounds like you're getting a few of the common problems with a 540 all at once!!