I started a parts list before we even touched the bike based on what I expected to find and was pretty darn close. Piston and rings, seals, gaskets, counterbalance shaft bearings.. ended up needing a few small extras like woodruff keys, plastic timing chain guide, and a few misc hardware items.
First step was an online bmw dealer parts search to get all the part numbers. Then googled the piston (most expensive and common part) to see whats out there. There didnt appear to be any aftermarket parts available for this engine. No problem since i really prefer to use OEM internal engine parts. Searching bmw part numbers returned mostly dealers and this place- http://www.2wheelpros.com
They sell tons stuff (OEM and aftermarket) for many motorcycle manufacturers. Overall their prices seemed about 10% less than bmw dealers. Some parts were backordered but thats ok since this is a winter project.
I did look into getting the C/B shaft bearings from a local brg supply place. BMW doesn't make bearings, they just repackage and mark up the price. These were standard size NTN brand bearings. After a long conversation at the brg supply place about brands and quality i ordered SKF brand (a huge worldwide bearing mfr). 2 days later i went to pick them up, and well, they just seemed low quality. Decided it was not worth using vs the cost savings. This engine will be 100% when im done and dont want any junk parts inside.
Lastly the water pump. No leaks but have heard lots of talk about issues here. BMW only sells a kit including seals, impeller, and shaft. My impeller and shaft have no wear but the seals a bit hard. A little research found the same seals are used in rotax go-kart engines. Ordered seals from a rotax dealer in Mass.