Twitching

[Fazerider]

If it's the rear of the bike that feels peculiar then perhaps that's where the problem is!
Have you checked things like worn swingarm bearings giving lateral play, or excess slop in the vertical direction caused by knackered bearings in the shock linkage? (Note there will be 2 or 3mm vertical play at the rear wheel even with new bearings in the shock linkage, more than that indicates a problem.)
The OE shock was never brilliant to start with and if there's a fair mileage on the bike, particularly if it's spent a good proportion of that heavily laden, then it may be worth trying a replacement.