I bought a full swap kit for my 325 for $120...tranny, used clutch, pedals, master & slave cyl, subframe, tranny mounts, shifter rod, etc... I'd put in a new clutch kit (~$250), a short-throw Z3 shifter (~$100) and replace all the rubber & plastic bits. Doing your own work with a bit of scrounging could make it even less than the $500 I'm spending.
If you farmed it out to a decent indie mechanic I'd guess it could be done for about $1000. Keep that in mind if the automatic fails.