New gaskets, seals, chain case parts and tensioner. I'd probably do the valve seals & have the guides checked by a decent performance shop. I'd be tempted to balance the crank & pistons too. I'd definitely clean out the ports a little, but not to hog them out...just a cleanup.
I'd also totally gut every piece of rubber in the engine. New coolant, fuel & vacuum lines. Maybe even an engine mount or two.
+1 on the stroker, it's the best time to think about that. It's also a good time to think about new seals on the tranny, guibo, mounts, etc...and new relays, O2, fuel pump.
You'd have a great new engine, built to your specs, that'll run another easy 100,000 miles. It'll cost you $3-4k to do it right. More with a stroker. Try to find a BMW with less than 100,000 miles and you'll know why it's worth it.