Idk if this will help you out, but I ended up converting my top to be manual after I found that the three studs coming out from the body (that the transmission is bolted to) were bent out of alignment. I was going crazy replacing each component; the transmissions, arms, Vs, cables, etc., but it was the actual mounting studs throwing everything off. I have zero issues with it being manual- stress free living.
https://986forum.com/forums/boxster-general-discussions/80023-99-boxster-roof-off-tracks-need-help.html