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Completely solved this, more or less as described above. 

using calibur, import your books

select all, download meta data and covers

select all, resize cover (this is a plugin) I use 300x432px (the ubooquity max i think)

select all, bulk convert, to epub

point your ubooquity server at your calibur database or copy all books to where you normally store your books

clear database in ubooquity

VOILA, all perfectly sized books

util.js:63 [Xirvik] Options was retrieved.

folderCover?folderinfo=series.json&_=1556377605390:1 Failed to load resource: the server responded with a status of 404 (Folder info resource not found or access not authorized)

themeScript.js:312 The above 404 just means there is no series.json for this page, it can be ignored. - ScooterPSU

it seems it something to do with the grouping. if set to folder, the green bar underneath issues disappears and there is also no way to bookmark an issue. 

no but most books are portrait, the aspect ratio could differ slightly. I've not seen a landscape Kindle yet at least :)

 

I think, looking at it. Ubooquity is ignoring the cover.jpg created by Calibre and is pulling the images from the epub file. I could use the calibre plugin resize xxxxx to give all the books a common size and then 're-convert' from epub to epub which should inject the cover. It would be easier I suppose if Ubooquity read the cover.jpg though

 

anyone any idea how this can be achieved?