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I would use a drill to create your hole in the main stem for the cut and i would use more of a thick branch like cut rather then a small end cut clone. Maybe something with bark as i would use the same size drill bit as the cut. You can always trim the cut down so the host plant doesnt have to take on such a big burden. By using a drill bit the size of your cut, it should fit nice and tight. Then i would use some sort of putty around the wound to seal up the drilled hole. It should keep it in place for ya too:thumbsup:
Now you could also drill your hole straight through the main stem, then remove the outer layer of a cut and slide the cut through the hole till your scraped cut matches up to the hole in the main branch. Now this works on trees, but never tried on a MJ plant, but id think the hole would heal with putty to enclose it.
One more thing to toss out. If you want a clone fast and a big one just scrap around the outer part of the cut you want to take. Then apply rooting gel to where you scrapped. Now add a medium in something like cheese cloth or pantyhose and wrap it around the area you had scrapped. In a week you will see the roots starting to form in the pantyhose. Then cut just below the new set of roots, unwrap the pantyhose and plant. Make sure the medium is against the scrapping and not the pantyhose, but im sure ya got that.
Back when I started this thread, VanceFish and Myself actually discussed exactly what you are talking about with drilling into a re-veged stump/root structure to "Plug" grafts in to it. (He had a rather large G-13 that he was Re-veging at the time, she's dead now cut into a million pieces and disposed of)
That "On plant" cloning idea is interesting! :thumbsup: You got any pics of doing that? (even if it's a tree, I don't care, just want to see exactly what your up to.)