You have a better chance of finding a manual Unicorn, tbh. There are a few around but other than in the introductory year or so, the numbers of manual versions didn't extend much beyond a bakers dozen in any of the permutations and combinations of body style and manual. The example below is probably one of the better auto's at the moment in the UK. In Ireland the numbers of 540i sold in e39 were tiny (a senior manager where I work had one back in the day as a co. car).

As for Japan, that's where many of the better ones being offered in the UK at the moment are coming from (see http://www.gmscars.co.uk/ for some example). I had a look at what was to be had in Japan about 2 years ago as I was heading to Japan on a trip in late 2016 and toyed with the idea of brining something back (didn't pursue it at the time, but not for lack of opportunities). Have a look at https://www.smilejv.com/auction/login_01_form.php - you'll need to register to see anything worthwhile. There were a reasonable number of low mile 540i's popping up, but, based on what I saw, I'd say a manual would be unheard of in Japan.

https://www.autotrader.co.uk/classif...to=2003&page=2

The one that got away, for me, was a 2001 540i Sport manual in the UK with a little over 1k miles about 10 years ago. It had been bought and kept in an underground car park in central London - presumably by an oil squillionaire who spent August in London or something. VRT at the time would have been about €21.5k as it would have been treated as a new car. Heading on a meandering trip to Bordeaux rather than Dublin, filling it with fine wine and taking the long way home would have brought the VRT down to €5.5k (plus the cost of the wine!). At the lower VRT figure it would have landed for low 20k's.