Sounds very tricky! Has the rear ride height been increased by adding preload or fitting a longer shock? That would change the unloaded chain line by the miracle of geometry. Some Ducatis such as the ST series had a ride height link that could be adjusted for quicker turn-in, but extra chain slack was needed to prevent the gearbox bearings being harmed on full bump. The ideal way to set chain tension is, of course, to load the rear until the swing-arm gives a straight run from sprocket centre to wheel centre and set it right there.
Nick