Alright... i'm getting somewhere.
I found something to replace the pin and got that in place, i used JB weld to keep the pin in place.
I then tightened the flower nut as tight as i could and then placed the cover in place over the ball and peg and tightened the screws evenly... as i tightened the peg and ball moved in more and i was able to tightened the flower nut more and more as i went. Eventually the cover sat flush... yay!! I placed the cover over the gear side and my repair of the casing looks pretty good i think
Its pretty late now, so tomorrow i will mount the engine back on my bike and test it out. Hopefully ill be up and running
Thank you everyone for your excellent advise.