I put mine in the way the one was oriented I took out. I'm pretty sure it was the original.

The recessed area was towards the internals of the engine and holding some oil.
 

The flat side was out, flush with the case.
 

Tough to tell in your diagram, but it appears #13 is the left side crank seal and #15 is the right side. #13 looks to be pointing the way I put mine in.

It looks correct to me but then again I'm not one of the resident experts here, I am learning though

Diagrams and even manuals sometimes have incorrect information. 

Original crank seal was a true SW dual lip dual spring seal with special properties.  Looks like a cheap generic single lip seal was installed on MX250.

One feature of original MX250 seal was the "castle turret bumps" that face in towards the bearing.  They prevent pressing seal in too far and cutting off oil to the bearing.  When the original seal is installed correctly, it does look "backwards" from the diagram.  As long as you don't press seal in to far it should be okay in that respect.  Aftermarket single lip might not seal as well as original..  And sometimes new seals leak.  I always pressure/vacuum test after installing seals or top end reassembly. 

From the other threads on this MX250 it most certainly has an air leak someplace.  My process for evaluating and testing a "new to me" engine or one with "runaway" issues is pressure and vacuum test to find and repair the leak(s).  Much cheaper and faster in the long run in my experience.  . 

I also would go with the original crank seal even though they can be hard to find and expensive for the earlier 250/360/400's. 

Original seal type:
 

MarkT, in your picture we are looking at the 'inward' facing side of the seal, correct?

I have a pressure tester on order that i'll rig up to tap into the spark plug hole. I'll run (my very first ever!) pressure/vac test and see if the crank seal is still leaking.