I don't know what shoes you're talking about, oem cork you mean?
Is your sprag clip intact? That will hammer your gears to bits is it's missing.
I don't run atf in anything, I like to run either 'motorcycle' 10w40 valvoline brand seems to be the most common, or rotella 15w40 diesel oil for the most slip.
I only have one tomos that has the stock cork shoes, stock a35, you almost can't even feel when it shifts. Downshifting is always tricky with tomos because of how the trans works, but it should never chatter or shudder.