OK, phoned a mate who is a motorcycle engineer, and he advised to put the new seal all the way in- he thought it might be so the sealing surface was in a slightly different position.
I rigged up a way of forming the teflon lip and fitting it.
Take a 3" plastic plant pot and carefully cut it to a size that will fit exactly over the end of the crank.
Using another identical pot, form the lip of the seal by sliding the seal on to the taper of the pot.
Take the seal off the pot after forming the lip, then put the cut bit over the uncut pot (for strength) and slide the seal on.
Remove the cut bit complete with seal and slide over the end of the crankshaft.
Remove former and gently tap the seal into place, making sure the lip is not deforming - it's quite stiff, so work quickly and you'll be fine. Job done. Quick eyeball and check with a depth guage and the flywheel can go on.
Oh, and in terms of the seal on the front end of the transmission, I found that the cap off a radiator valve (the one you need a spanner to turn off) with the top cut off is the exact size to slide over the splines. I put the seal on the cap and then slid it down the splines. Because of the ectra thickness of the plastic the seal popped in very easily. Again, quick check as there is no shoulder to make sure it's square to the bore.
