Some people have pulled the two pieces apart, cut both down and then reassembled with glue or RTV. Depending on how deep the shaft is still penetrating into the top portion this can still provide and extremely strong bond. If you've shortened it significantly I'd grind/melt/dissolve the original rubber, texture the inner rod and fill it like they did stock with a HIGH SHORE, two part urethane. I would use something with a little give though, not too rigid.
No, the inner rod is too thin do thread for a stock shifter. Either use a universal, thread for a different shifter, weld on a bolt end with the desired thread or reassemble like a stock assembly.
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