After spending a bit of time with this organ, one thing that strikes me is how good it sounds in meantone. Whenever I have changed the temperament of any other English organ I have to quarter comma meantone, it has sounded hideous (all of them Victorian, of course!), but this one sounds quite good in its current tuning. I had not actually read much about what temperament we would expect English organs to be in the 1690's, so I did a bit of an internet search. I found this thesis by John Meffen from 1973 which is very interesting:
http://etheses.dur.ac.uk/10096/1/10096_6890.PDFHe makes a very good argument that at the time, basically every organ, harpsichord and other instrument were probably tuned to quarter comma meantone. The one piece that seems like the gnat in this theory's eye is John Bull's Chromatic Fantasia, which he argues was written for a specific instrument that had 19 keys to the octave (since all 19 keys are called for and necessary for it to sound good, and John Bull probably encountered that instrument through his connection to Antwerp). So, this tuning for the instrument is probably the closest to what it was designed for. He also argues pretty convincingly that based on the music that was to be sung at church it is likely all organs at this time were meantone, and also very likely that virginals/harpsichords, etc. prior to the civil war were likely all meantone.
Of course, Bach's well tempered clavier came out in 1722, and in Europe by then there was starting to be some interest in many of the different well tempered schemes including Werkmeister's. However, at the time of this instrument's construction, there wasn't really any English keyboard music written that would really have made use of any of these well temperaments, and Meffen describes how even though equal temperament was known about, it was considered rather distasteful. England had just emerged from the civil war, when practically every organ in England had been destroyed, and the English organ building traditions had mostly been forgotten. When the first German organ builders arrived and tried to make instruments as close to the old "English" tradition as they could, they would have still been accustomed to meantone instruments back in Germany (starting after the restoration in the 1660's).
So it would seem, at least at this early date, meantone would have been the way to go, and no wonder it sounds so good in it! Now, it would be lovely to have more English Georgian Hauptwerk instruments to compare to!