Regarding driving the seal in backwards, you are correct, it must be done carefully. I find that if you clean the area very well, you can push the seal home with an appropriate sized tube. Many times I find the outer cover to be a rather loose fit. This is why I always use a small smear of RTV to assure a seal to the outside of the lip seal. If your outer cover is particularly tight, you might try warming the cover first, then push the seal home. Of course the alternative is to machine the outside of the cover for the MkIII style seal driven in from the outside.
Regardless of how you install the seal, care must be taken when installing the cover to avoid damaging the seal as the kickstart shaft is passed through.