You should be able to do this. I’ve done similar with my Indigo 2 sending notes to OT. I’m also using a midi solutions quad thru box to send from OT to everything.
Set your BS2 to send on the Midi Auto channel set on the OT.
Make sure all of the other devices don’t use the same channel. Just to be safe.
Set up your midi tracks in the OT to match the other device channels.
Make sure the Audio channel Midi CCs are off. The manual says this doesn’t seem to matter. Just to be sure.
I would use one keyboard as the input to OT. Then select the track that is set to the channel of the other keyboards on the OT. Learn the auto channel feature, it’s great!
Start simple. Set up the OT with BS2 first (the x4 might be a better kb?). Mess around with the settings, channels, etc. until the feedback loop stops. Then start adding the other pieces. I don’t think it will be possible to have all keyboards for note input.
Maybe one keyboard > MPD > OT > thrubox > everything (including keyboard).
I would just use transport to run the MD and not use the controller to it. It already has controls!
I hope these help.
Edit: Page 128 of the manual.http://www.elektron.se/sites/default/files/products/files/octatrack_manual_OS1.25.pdf