Was attempting to do a handle swap on my zillion. after some different approaches to undoing the nut on top of the handle, i finally got it to turn. when it was turning but not rising i finally realized that turning it clockwise made it rise. its a lefty retrieve. now there are some metal shavings loose but the shaft looks relatively intact and no discerning lines messed up to my untrained eye. Should i continue with the handle replacement or let the local tackle shop switch out the shaft? as long as just the nut is messed up, i am fine because the replacement handle came with one.

I would consult with Delaware Valley Tackle. He fixed my JDM Zillion for a nominal fee. I wouldn’t think twice about it.

If the mainshaft threads are fine, you only need a new nut. It's standard practice to make nuts from softer metal, so they will strip first.

If the mainshaft threads are damaged, you need a mainshaft.

one option is Plat.jp

https://www.plat.co.jp/shop/catalog/partsorder.php?products_id=4068

If you go to that much trouble, throwing in a brass HD gearset is only $35 on your order.

The threads in the picture don’t look damaged from what I see. I am not an expert, but if you were going to change the handle I would just put the new one on with the nut included.

Looks like you got lucky. Mainshafts can and do get stripped. Try a new nut making sure it starts easily and snug by hand. Tighten just enough to align the retainer with the screw hole. Don’t force it at all ever.