I've debated this a thousand times in my own head now that I have the engine out. I finally decided that I'm going to do it exactly how I've always done it. The pot joint installed into the diff and then drop in the engine. Then slide the driveshafts through and in with the boots attached to the shaft. Wrap around the pot joint and then put on a new zip tie. Worked well in the past and I think it will work well with a fresh engine. Much easier than trying to stab it in all as one piece IMO.

There are a few ways to do it, depending on whether the engine is out....   You can always install all from the outside with the engine IN the car... obviously the CV or Pot unit will not fit through the subframe like the yoke type, but still, with the engine bolted in, you can just pop the pot into the diff, then feed in the axle shaft from the outside and fully seat the spline. This is all done before the ball joints.

If the engine is out, you can have the fully assembled drive shafts (and all ball joints in place) ready to lift up to meet the diff flanges and get them started as you lower the engine. when it's all the way down the axles should be just about fully inserted into the diff.

I had guessed the problem when you first posted about "losing drive"... are you by chance running negative camber lower arms?  I've noticed that with my super-low 66 s- my lower arms are parallel to the ground, forcing the axle to operate at it's maximum length- I already have negative camber with the stock arms.  Longer arms (negative camber arms) would really be testing those splines as the axles would start to become too short to reliably stay in their splines!

Here is a short video from my CooperRoadMini of me popping them out to remove an engine from a Mark 1 S clone:

//cooperroadmini.com/2014/03/13/disconnecting-the-shift-linkage-and-axles-on-a-rod-change-classic-mini-cooper/

Here the third short video of this post (titled "Engine Back IN") shows me putting the engine back in, bringing the assembled axles up to meet the engine/gearbox:

//cooperroadmini.com/2014/03/31/getting-the-car-ready-and-the-engine-back-in/

Don't know if its the "proper" way.. However, IMHO the easist way is to remove the inner pot joint boot ties, undo the upper hub ball joint and allow the hub to fall outwards. 

This will pull the inner pot jint inner from the outer shell - which remains attached to the gearbox.  Place some rags under the inner joint area in case any of the ball fall out of the inner race.

On reassmbly, coat the balls in grease and stick them into the inner race. Wrap the inner joint section in a single layer of plastic kitchen wrap (Glad Wrap) to keep it clean/ensure all the ball reamin in place.

Once the engine is in place, line up the inner and outer sections of inner joint (you may have to rotate the drive shaft to ensure the balls line up with their respective grooves).

Lift the hub and connect up the upper ball joint - this will push the inner and outer sections of the inner joint together.

Re-attach to boot.

On subsequent dissassembly of the joint you may find remnants of the plastic wrap still inside the joint but this has never caused a problem with the joint's operation...

Cheers, Ian

You did it the way I do now.  I've battled the assembled drive shafts onto the output shafts of the differential many times and it was never easy.  Inserting the drive shaft with the CV balls and cage in place is messy for sure, but it allows me to know that all of the spring clips are expanded and in the right place.  Don't the manuals state the drive hubs need to have the lower ball joints released to swing them out from the lump allowing the pot joints to be pulled out of the diff before the lump is removed (reassembly is the reverse)?

Looking for the best method to re-install or re-assemble the pot joint style drive line.

In the past when I had an engine out I would install the complete and booted pot joint onto the output shaft.

I would place the drive shaft with outboard CV properly attached into the hub, raise the hub to get the geometry right and tap the assembly into the pot joint. This means you cannot really test if the shaft is seated properly in the pot joint internals as it is diffcult to apply pressure to try to remove it from the internals.

On my most recent re-assembly after failing to seat the shaft correctly, I seated the pot joint internals onto the drive shaft and then inserted the pot joint internals into the pot and attached the boot. I managed to get grease all over the LCB which needed to burn off. I was at least able to verify that both CVs were seated correctly with this method.

Terry