I went through the same things as you are going through when i bought my XR some years ago. MIne had the 440cc kit, heavy duty clutch drilled air box, snorkel removed, hugely jetted up then one day outwent out to practise filled up with fuel somethig went bang and i found this.
When i rebuilt it i put it back to a standard 400 as these motor can't cope with the 440 kits i've not heard of any that live very long using these kits this was fitted to the bike when i bought it and i wasn't told about it or i would have walked away. This one was the weisco 12.5:1 kit (high compression). The over revving was what caused the rod to fail. After the bike was put back to standard it went for quite a few hard years of use effortlessly untill it started smoking, then i opened it up pressed and cut a new set of valve guides in it, new valves seals fitted, cut the valves to suit the new seats then lapped them in threw it back together and like a new one. Then shortly after the wife got pregnant so i sold it and my beloved GAsgas EC250 gave up competion racing and now i only have my Trials bike and Varadero. Now waiting for the baby to be 2 years at next Christmas and he can have his new little OSET as soon as he's walking.
absolutly loved my XR one of the best bikes i've owned and wish i never sold it, that was a big mistake the punishment they can take and pleasure they give is unreal
This is what came out after i flushed it and it ran sweet as a nut