Picked up my xt660r a month ago and it's totally stock. Fuelling felt ok if a little hesitant at low revs and a bit of surging at constant throttle.

A friend has a CO meter so we removed the snorkel and looked at the fuelling. CO was 0.6% standard with snorkel removed which is way too lean. A look at the CO in diag mode and it was set at 6 so we increased it 10 points and this increased the CO by 1% so we oncreased it another 10 points and left CO at 2.6% which is a lot better and maybe a touch high for the cats....
Bike rode better but there is still some surging especially when trying to control the throttle for balancing on one wheel, it felt like it wanted more fuel but didn't really want to increase it with the cats still in exhausts. So next step was to re-fit the snorkel and trim the CO back by 10 points. It is now all stock and the only mod is increasing fuel 10 points.

This is much better, holds a constant throttle even at very low speeds and is happy to fuel with tiny throttle openings on one wheel.

I guess if you have tried all sorts it may be worth returning to stock and just trying a bit more fuel from the diag mode