After doing some more research, I've decided to skip the oil catch can and fit a PCV valve instead. That should make for a cleaner and simpler install. 

Thanks to prodding by buffalo, I think I've found some vacuum lines that may work.

I removed the vacuum rail off the throttle bodies. Contrary to what I would have thought, it was easy to pull off even without disturbing the host clamps. I thought it would be hard plastic but it turns out it's just molded rubber. Fortunately, it turned out to be in good shape.

I carefully removed the hose clamp on the rear end of the rail. It was challenging because it is far too easy to damage the rubber piece, but after some time I managed to get a screwdriver under the lip where it was folded over so that I could pry the hose clamp off. 

I pulled the end cap out and then simply pulled the little plastic adapter from the angled part and put the cap in there and then inserted the plastic adapter piece to the end where I had just removed the cap.

Now I have a nice vacuum rail with an adapter out the rear that will allow me to avoid having to do crazy hose routing. It also means I can get access to it with the frame on the bike. 

Finding flexible 12mm inner diameter host to use for this connection is proving just a little challenging. I still need to find 16mm inner diameter hose for the crankcase breather. 

Before:
after:

I've been thinking about how to route the hose from the black vacuum rail on the back of the throttle bodies. It's 1/2" and because of the angle of the adapter, it requires a pretty serious bend and some cutting of the insulating material to get it to route back to the battery box. 

Instead of doing this, I had the idea today that maybe it would be better to replace the rail with some 1/4" tubing and T-Connectors. Then I could just run the line straight to the rear. 

The existing tube comes off distressingly easily. I pondered flipping the tube around to angle the adapter to the rear but there doesn't seem to be enough room. 

It may also be possible just to cap off the adapter towards the front and pop the end cap off to insert a fitting. That might be an even better solution.

We got the smaller hose run from the front of the engine to the battery box area where the oil canister will be mounted.

The hose I bought for the vacuum line is too stiff to route. I'm not yet sure what to do about that. I had the idea that maybe I should remove plastic tube and using some small sections of tubing and T connectors fashion my own. It would make the routing much cleaner. 

The hose I bought for the rear crankcase vent is also too large so I'll have to find some alternative. 

We did manage the get the air box sealed up using a couple of the rubber stoppers along with RTV Black gasket maker.

Ok, so it looks like this is probably the best solution as it essentially just moves the "cyclonic separator" out of the airbox and puts it where it can be drained regularly. It looks like this mirrors the stock setup more closely and means that, if I understand correctly, the behavior of the engine vacuum will much more closely match the stock profile.

Thanks to Mateusz Wojciech in the BMW K100 Purists group for the suggestion, photo, and responses. The hoses are routed as follows:

"one thinner to timing gear ( 6mm ), bigger to crank case(blue colour on the photo), and second bigger to throttles(black)"

I think, barring any new information, that going with the racing catch can solution might be the best option.