I'd want to put a modern 6 or more speed ZF type auto behind that engine (excellent choice, by the way). Obvious sources are a Merc or BMW, preferanly a diesel, so as to get roughly the right change up speeds and TQ convertor stall speed. But mating to the engine is going to need to be fairly inventive! I'd start by getting a crank spigot and flex plate (pray they didn't use dual mass flywheels on L series autos!) from an L series auto. Neither of the gearboxes you have I would rate as remotely suitable.
I wouldn't worry too much about the transmission tunnel. Get the correct drivetrain first. If it turns out to be a bit tight, then you can graft a P6 auto tunnel in relatively easily. There are generally an adequate supply of rusted out 2200 autos to supply a donor.
Other significant consideration is the engine mountings. Position and stiffness of the engine mounts makes a hige difference to how liveable with your diesel will be. I presume your L series is going to be from a trasverse installation, so the current layout of it's mounts is going to be plain wrong - one of them is likely to be off the nose of the engine towards what is now the bonnet slam panel - not a strong point of the P6! I suggest robbing the mountings (including a portion of the body where they attach) from whatever inline installation you get the gearbox from. Then try and position them in roughly the same location on the L series.
For a sump I'd put money on a sump drom any O series or Pinta inline installation suiting
Chris